[1] "ofn"        "-oTSTES-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/STES-TP/15090071/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/15101925/transformed.cor.cli.txt"

nPatients in clinical file=612, in cluster file=625, common to both=609
[1]  99 609
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            98                            511 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            98                            511 
[1] "AMP PEAK  2(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           92                           517 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           92                           517 
[1] "AMP PEAK  3(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          238                           371 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          238                           371 
[1] "AMP PEAK  4(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          234                           375 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          234                           375 
[1] "AMP PEAK  5(2Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          148                           461 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          148                           461 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          276                           333 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          276                           333 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           217                            392 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           217                            392 
[1] "AMP PEAK  8(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          205                           404 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          205                           404 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          185                           424 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          185                           424 
[1] "AMP PEAK 10(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        137                         472 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        137                         472 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        108                         501 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        108                         501 
[1] "AMP PEAK 12(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          344                           265 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          344                           265 
[1] "AMP PEAK 13(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          330                           279 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          330                           279 
[1] "AMP PEAK 14(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          309                           300 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          309                           300 
[1] "AMP PEAK 15(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          225                           384 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          225                           384 
[1] "AMP PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           266                            343 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           266                            343 
[1] "AMP PEAK 17(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           441                            168 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           441                            168 
[1] "AMP PEAK 18(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           88                           521 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           88                           521 
[1] "AMP PEAK 19(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          124                           485 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          124                           485 
[1] "AMP PEAK 20(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          180                           429 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          180                           429 
[1] "AMP PEAK 21(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            166                             443 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            166                             443 
[1] "AMP PEAK 22(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           124                            485 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           124                            485 
[1] "AMP PEAK 23(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            119                             490 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            119                             490 
[1] "AMP PEAK 24(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         133                          476 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         133                          476 
[1] "AMP PEAK 25(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           209                            400 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           209                            400 
[1] "AMP PEAK 26(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           201                            408 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           201                            408 
[1] "AMP PEAK 27(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         158                          451 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         158                          451 
[1] "AMP PEAK 28(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           211                            398 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           211                            398 
[1] "AMP PEAK 29(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           238                            371 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           238                            371 
[1] "AMP PEAK 30(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           106                            503 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           106                            503 
[1] "AMP PEAK 31(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           162                            447 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           162                            447 
[1] "AMP PEAK 32(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         216                          393 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         216                          393 
[1] "AMP PEAK 33(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            171                             438 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            171                             438 
[1] "AMP PEAK 34(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           192                            417 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           192                            417 
[1] "AMP PEAK 35(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                            76                            533 
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                            76                            533 
[1] "AMP PEAK 36(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                         181                          428 
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                         181                          428 
[1] "AMP PEAK 37(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                            157                             452 
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                            157                             452 
[1] "AMP PEAK 38(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                           407                            202 
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                           407                            202 
[1] "AMP PEAK 39(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                        146                         463 
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                        146                         463 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           203                            406 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           203                            406 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          150                           459 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          150                           459 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         45                         564 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         45                         564 
[1] "DEL PEAK  4(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         43                         566 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         43                         566 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          118                           491 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          118                           491 
[1] "DEL PEAK  6(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           84                           525 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           84                           525 
[1] "DEL PEAK  7(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           81                           528 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           81                           528 
[1] "DEL PEAK  8(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          118                           491 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          118                           491 
[1] "DEL PEAK  9(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          237                           372 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          237                           372 
[1] "DEL PEAK 10(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          269                           340 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          269                           340 
[1] "DEL PEAK 11(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           96                           513 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           96                           513 
[1] "DEL PEAK 12(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            62                            547 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            62                            547 
[1] "DEL PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          263                           346 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          263                           346 
[1] "DEL PEAK 14(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          260                           349 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          260                           349 
[1] "DEL PEAK 15(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          290                           319 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          290                           319 
[1] "DEL PEAK 16(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          292                           317 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          292                           317 
[1] "DEL PEAK 17(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          271                           338 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          271                           338 
[1] "DEL PEAK 18(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          182                           427 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          182                           427 
[1] "DEL PEAK 19(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          142                           467 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          142                           467 
[1] "DEL PEAK 20(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        149                         460 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        149                         460 
[1] "DEL PEAK 21(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          125                           484 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          125                           484 
[1] "DEL PEAK 22(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          162                           447 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          162                           447 
[1] "DEL PEAK 23(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          200                           409 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          200                           409 
[1] "DEL PEAK 24(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        292                         317 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        292                         317 
[1] "DEL PEAK 25(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          320                           289 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          320                           289 
[1] "DEL PEAK 26(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           171                            438 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           171                            438 
[1] "DEL PEAK 27(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           125                            484 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           125                            484 
[1] "DEL PEAK 28(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             95                             514 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             95                             514 
[1] "DEL PEAK 29(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                           106                            503 
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                           106                            503 
[1] "DEL PEAK 30(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                           128                            481 
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                           128                            481 
[1] "DEL PEAK 31(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                            175                             434 
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                            175                             434 
[1] "DEL PEAK 32(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                           170                            439 
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                           170                            439 
[1] "DEL PEAK 33(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                         168                          441 
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                         168                          441 
[1] "DEL PEAK 34(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                           110                            499 
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                           110                            499 
[1] "DEL PEAK 35(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                           104                            505 
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                           104                            505 
[1] "DEL PEAK 36(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                            131                             478 
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                            131                             478 
[1] "DEL PEAK 37(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                           119                            490 
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                           119                            490 
[1] "DEL PEAK 38(13Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                            120                             489 
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                            120                             489 
[1] "DEL PEAK 39(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                           183                            426 
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                           183                            426 
[1] "DEL PEAK 40(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                            186                             423 
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                            186                             423 
[1] "DEL PEAK 41(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                           178                            431 
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                           178                            431 
[1] "DEL PEAK 42(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                           175                            434 
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                           175                            434 
[1] "DEL PEAK 43(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                           146                            463 
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                           146                            463 
[1] "DEL PEAK 44(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                           259                            350 
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                           259                            350 
[1] "DEL PEAK 45(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                         258                          351 
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                         258                          351 
[1] "DEL PEAK 46(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                           102                            507 
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                           102                            507 
[1] "DEL PEAK 47(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                           283                            326 
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                           283                            326 
[1] "DEL PEAK 48(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                           313                            296 
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                           313                            296 
[1] "DEL PEAK 49(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                           242                            367 
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                           242                            367 
[1] "DEL PEAK 50(19Q13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                            118                             491 
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                            118                             491 
[1] "DEL PEAK 51(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                            70                            539 
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                            70                            539 
[1] "DEL PEAK 52(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                           280                            329 
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                           280                            329 
[1] "DEL PEAK 53(21Q22.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                            294                             315 
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                            294                             315 
[1] "DEL PEAK 54(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                           224                            385 
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                           224                            385 
[1] "DEL PEAK 55(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                            231                             378 
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                            231                             378 
[1] "DEL PEAK 56(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                          143                           466 
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                          143                           466 
[1] "DEL PEAK 57(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                          136                           473 
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                          136                           473 
[1] "DEL PEAK 58(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                          138                           471 
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                          138                           471 
[1] "DEL PEAK 59(XQ11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                           98                           511 
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                           98                           511 
[1] "DEL PEAK 60(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                            94                            515 
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                            94                            515 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "NUMBER_PACK_YEARS_SMOKED"              
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 609 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=197,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=323,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=34,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 609 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "NUMBER_PACK_YEARS_SMOKED"              
[10] "COMPLETENESS_OF_RESECTION"             
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
[13] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  52 126 280 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53   126   280   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  52 126 280 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53   126   280   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
200 182  96  97 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
200 182  96  97 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
200 182  96  97 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
200 182  96  97 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=34, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P36.22) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  1(1P36.22) MUTATED    56  38
  AMP PEAK  1(1P36.22) WILD-TYPE 298 183
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            94                            481 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            38                            183 
$`AMP PEAK  1(1P36.22) MUTATED`
TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A8O2 
        7.69        20.78         3.88        17.03         0.79         4.67 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A88Y 
       42.77        25.22        47.93        18.35         3.16         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NS 
        3.95         3.02        55.50         2.66        13.48        13.41 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A9FO 
       10.45        12.66        13.15         0.10         0.10         0.13 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        8.02        14.70        29.59        53.95         9.30        15.78 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-VR-AA7B TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-7197 
       12.69        20.02        11.24         2.10         6.61         9.21 
TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-A4CQ 
        3.45        12.95         2.66        25.18        12.79        22.26 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-A48A TCGA-CD-A4MH 
        0.72        13.51         3.25         0.30        12.43        12.20 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5732 
       29.98        47.05        19.07        22.98        36.00        69.04 
TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 
       18.54        10.26        15.22        16.44        11.24         2.96 
TCGA-FP-7829 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       19.53        18.08        26.47        11.77         8.98         6.25 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42        21.21         3.45        18.38         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 
        6.74         1.81         2.53         9.24         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
       37.91       115.69         5.46        18.48        35.24        22.19 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-A92D 
       17.85         1.87        64.57         1.71         4.54        64.18 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       42.54        18.41        32.94        17.13 

$`AMP PEAK  1(1P36.22) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF 
       13.94         8.94        16.24         4.21        32.45         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        23.41        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
       25.12         7.40        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       83.24        52.57        46.09        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       13.41         0.10        15.35        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 
       10.52        12.00        12.23        12.03        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
        5.16         7.82         7.59         5.06         7.04         6.35 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       30.71        18.18        42.87        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       15.91        10.16         3.42         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        12.76        18.71        17.49        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-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-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-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-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-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       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        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        15.16        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        8.81        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51         5.56         7.82        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.25        13.02        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50        12.79         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        26.24        27.35        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        9.04         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        11.24        22.09        40.08        28.41        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                         12.87                          12.76 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P36.22) MUTATED         2        6        6        7         9
  AMP PEAK  1(1P36.22) WILD-TYPE       9       13       42       25        68
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED          13         2         17         12
  AMP PEAK  1(1P36.22) WILD-TYPE        71        27         80         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P36.22) MUTATED            6        6         2
  AMP PEAK  1(1P36.22) WILD-TYPE         42       45         2
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               2                              9
  STAGE IA                              6                             13
  STAGE IB                              6                             42
  STAGE II                              7                             25
  STAGE IIA                             9                             68
  STAGE IIB                            13                             71
  STAGE III                             2                             27
  STAGE IIIA                           17                             80
  STAGE IIIB                           12                             60
  STAGE IIIC                            6                             42
  STAGE IV                              6                             45
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK  1(1P36.22) MUTATED      14  19  45  13
  AMP PEAK  1(1P36.22) WILD-TYPE    39 107 235 111
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T0+T1                           14                             39
  T2                              19                            107
  T3                              45                            235
  T4                              13                            111
[1] 4 2
[1] TRUE
[1] "dimension of 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    30  29  16  16
  AMP PEAK  1(1P36.22) WILD-TYPE 170 153  80  81
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           30                            170
  N1                           29                            153
  N2                           16                             80
  N3                           16                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    79   5
  AMP PEAK  1(1P36.22) WILD-TYPE 434  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     79    5
  AMP PEAK  1(1P36.22) WILD-TYPE  434   34
   clus
vv  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  0                           79                            434
  1                            5                             34
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    16  82
  AMP PEAK  1(1P36.22) WILD-TYPE 166 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     16   82
  AMP PEAK  1(1P36.22) WILD-TYPE  166  345
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           16                            166
  MALE                             82                            345
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  1(1P36.22) MUTATED                                       9
  AMP PEAK  1(1P36.22) WILD-TYPE                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                       22
  AMP PEAK  1(1P36.22) WILD-TYPE                                                    140
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P36.22) MUTATED                                                                  16
  AMP PEAK  1(1P36.22) WILD-TYPE                                                                65
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                 10
  AMP PEAK  1(1P36.22) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                          3
  AMP PEAK  1(1P36.22) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  1(1P36.22) MUTATED                                                           1
  AMP PEAK  1(1P36.22) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  1(1P36.22) MUTATED                                          2
  AMP PEAK  1(1P36.22) WILD-TYPE                                       11
D1V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK  1(1P36.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     0  98
  AMP PEAK  1(1P36.22) WILD-TYPE   6 505
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      0   98
  AMP PEAK  1(1P36.22) WILD-TYPE    6  505
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                             0                              6
  YES                           98                            505
[1] 2 2
[1] FALSE
D1V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  1(1P36.22) MUTATED    51   2   2   3
  AMP PEAK  1(1P36.22) WILD-TYPE 296  16  17  22
D1V11, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  R0                           51                            296
  R1                            2                             16
  R2                            2                             17
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P36.22) MUTATED      19                         1
  AMP PEAK  1(1P36.22) WILD-TYPE   110                        12
                                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      67
  AMP PEAK  1(1P36.22) WILD-TYPE   318
D1V13, multiclass
                                           clus
vv                                          AMP PEAK  1(1P36.22) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               67
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                110
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     2  61
  AMP PEAK  1(1P36.22) WILD-TYPE   5 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      2   61
  AMP PEAK  1(1P36.22) WILD-TYPE    5  333
                        clus
vv                       AMP PEAK  1(1P36.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       AMP PEAK  1(1P36.22) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            333
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1P34.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1P34.2) MUTATED    52  36
  AMP PEAK  2(1P34.2) WILD-TYPE 302 185
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           88                           487 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           36                           185 
$`AMP PEAK  2(1P34.2) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3YA TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A93E 
        8.94        20.78        17.03         4.67       122.10        25.22 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A891 
       47.93        18.35         1.38         7.13         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-LN-A49L 
        3.02         2.66        13.22         5.49        13.41        10.45 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-LN-A9FO 
       13.15        13.25         0.10        11.54        12.03         0.13 
TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC 
        8.02        29.59         6.35        53.95        12.69         3.42 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-AA7B TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       19.96        22.82        28.11        11.24         2.10        19.73 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-7901 
        9.44         6.61        18.35         9.57        19.33         3.45 
TCGA-BR-8286 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       12.95        25.18        12.79         0.72        13.51        20.65 
TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A48A TCGA-CG-4444 TCGA-D7-5579 TCGA-D7-6521 
       13.64         0.07        12.43        47.05        11.93        18.54 
TCGA-D7-6527 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-EQ-A4SO TCGA-F1-A72C 
       10.26        18.21        14.27        16.44        16.24        11.38 
TCGA-FP-7829 TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GF TCGA-HU-A4GH 
       19.53        17.06        26.47         5.92        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
        8.98         6.25        18.38         6.44         6.74         1.81 
TCGA-KB-A6F7 TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-VQ-A8DU 
       60.56         6.08       122.30       115.69        71.38         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PH TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A922 
       18.48        35.24        12.79        27.35        65.16         9.04 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       42.54        18.41        32.94        17.13 

$`AMP PEAK  2(1P34.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
        9.96        14.86        14.50        12.16        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90        29.00         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        2.60        25.12         7.40        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        13.41         0.10        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 
       25.25        10.52        12.00        12.23        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         7.59         5.06        14.70         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
       18.81        12.43         1.55        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        46.19        15.06         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       10.16         3.42         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.01         9.47         6.97         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-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        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46        20.42         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        11.31        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        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-D7-6815 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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34         7.40         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-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-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-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
       13.08         1.41        12.59         6.51         5.56         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       37.91        40.64       116.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        26.24        64.57        14.33        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       36.16         7.36         9.50         9.73        52.24         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        11.24        22.09        40.08        28.41        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       13.185                        12.620 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1P34.2) MUTATED         3        2        2        4        11
  AMP PEAK  2(1P34.2) WILD-TYPE       8       17       46       28        66
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1P34.2) MUTATED          11         7         19         10
  AMP PEAK  2(1P34.2) WILD-TYPE        73        22         78         62
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1P34.2) MUTATED            6        4         2
  AMP PEAK  2(1P34.2) WILD-TYPE         42       47         2
D2V3, multiclass
            clus
vv           AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             2                            17
  STAGE IB                             2                            46
  STAGE II                             4                            28
  STAGE IIA                           11                            66
  STAGE IIB                           11                            73
  STAGE III                            7                            22
  STAGE IIIA                          19                            78
  STAGE IIIB                          10                            62
  STAGE IIIC                           6                            42
  STAGE IV                             4                            47
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  2(1P34.2) MUTATED      12  13  44  14
  AMP PEAK  2(1P34.2) WILD-TYPE    41 113 236 110
D2V4, multiclass
       clus
vv      AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  T0+T1                          12                            41
  T2                             13                           113
  T3                             44                           236
  T4                             14                           110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  2(1P34.2) MUTATED    24  32  14  12
  AMP PEAK  2(1P34.2) WILD-TYPE 176 150  82  85
D2V5, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  N0                          24                           176
  N1                          32                           150
  N2                          14                            82
  N3                          12                            85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    75   3
  AMP PEAK  2(1P34.2) WILD-TYPE 438  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     75    3
  AMP PEAK  2(1P34.2) WILD-TYPE  438   36
   clus
vv  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  0                          75                           438
  1                           3                            36
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    21  71
  AMP PEAK  2(1P34.2) WILD-TYPE 161 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     21   71
  AMP PEAK  2(1P34.2) WILD-TYPE  161  356
        clus
vv       AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  FEMALE                          21                           161
  MALE                            71                           356
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  2(1P34.2) MUTATED                                       6
  AMP PEAK  2(1P34.2) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1P34.2) MUTATED                                                       23
  AMP PEAK  2(1P34.2) WILD-TYPE                                                    139
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1P34.2) MUTATED                                                                   7
  AMP PEAK  2(1P34.2) WILD-TYPE                                                                74
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  2(1P34.2) MUTATED                                                 13
  AMP PEAK  2(1P34.2) WILD-TYPE                                               65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  2(1P34.2) MUTATED                                                          4
  AMP PEAK  2(1P34.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  2(1P34.2) MUTATED                                                           1
  AMP PEAK  2(1P34.2) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  2(1P34.2) MUTATED                                          2
  AMP PEAK  2(1P34.2) WILD-TYPE                                       11
D2V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  2(1P34.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  2(1P34.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            74
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED     1  91
  AMP PEAK  2(1P34.2) WILD-TYPE   5 512
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED      1   91
  AMP PEAK  2(1P34.2) WILD-TYPE    5  512
     clus
vv    AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  NO                            1                             5
  YES                          91                           512
[1] 2 2
[1] FALSE
D2V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P34.2) MUTATED    44   4   0   5
  AMP PEAK  2(1P34.2) WILD-TYPE 303  14  19  20
D2V11, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  R0                          44                           303
  R1                           4                            14
  R2                           0                            19
  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"
D2V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1P34.2) MUTATED      18                         3
  AMP PEAK  2(1P34.2) WILD-TYPE   111                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1P34.2) MUTATED                                           0    63
  AMP PEAK  2(1P34.2) WILD-TYPE                                         1   322
D2V13, multiclass
                                           clus
vv                                          AMP PEAK  2(1P34.2) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          AMP PEAK  2(1P34.2) WILD-TYPE
  ASIAN                                                               111
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED     1  58
  AMP PEAK  2(1P34.2) WILD-TYPE   6 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED      1   58
  AMP PEAK  2(1P34.2) WILD-TYPE    6  336
                        clus
vv                       AMP PEAK  2(1P34.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK  2(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           336
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q21.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q21.3) MUTATED   132  89
  AMP PEAK  3(1Q21.3) WILD-TYPE 222 132
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          221                           354 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                           89                           132 
$`AMP PEAK  3(1Q21.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE 
       31.27        58.55         7.63        13.94        16.24         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.09         0.85         2.63        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        23.41        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH 
      122.10         3.68        31.56        25.22         0.30        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OT 
       19.99        21.01        47.93        18.35         7.17         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
       55.50         2.66        12.92        16.47        13.22         5.49 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A49V 
       13.41        52.57         5.92        10.45        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.25        12.59        12.49        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
        4.47        12.33        12.00        13.18         0.13         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.06        14.70        29.59         6.35        53.95        15.78 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EQ 
       12.69        20.02        20.38         3.42         4.80        22.82 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN 
        8.12        28.11        15.91        10.16         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 
       19.73        11.01         9.44         6.61        17.29        19.33 
TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
       25.61         9.21        18.15        28.73         3.45        11.44 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8373 
       12.95         2.66         2.20         6.18        14.04        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        0.26         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 
       12.79        15.81         8.22         0.72        12.82        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8524 
       20.65        20.42         1.15        13.64        13.15         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.10         0.13         0.16         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42         9.34        12.43        11.61         6.58        12.20 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
        7.99        54.08        47.05        21.99        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 
       12.00        22.98        36.00        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-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT 
       10.55        11.31        12.33        24.72        19.50        14.27 
TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 
       16.44        11.24        11.31         2.96        15.65         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 
        7.99        16.24        72.23         3.48        14.07        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         5.52        18.08        26.47         5.92        14.27 
TCGA-HU-8245 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.59         3.25        22.75        25.81        11.77         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
        6.51         6.25        12.95        12.30        27.42         3.45 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       18.38         5.19         1.41         6.44         6.74         1.81 
TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       60.56        18.21         6.08         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX 
       18.48        35.24        21.73         2.70        17.85        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        65.16        36.69        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
       36.16         9.73         4.54        64.18        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6K 
       22.09        18.41        40.08        32.94        12.43 

$`AMP PEAK  3(1Q21.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        14.30         5.92         8.94         4.21        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A6QS 
        6.21        33.27        20.78        20.12         9.30         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
        4.70         3.32         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NI 
        7.13         6.94         8.71        25.12        35.97        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
       13.55         7.76        21.37         8.71        27.12        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.15         0.10        12.46        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        0.10        15.52        25.25        10.52        12.23        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y2 
       33.11         5.16         7.82         7.59         7.04         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        2.89         1.45         7.00         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        9.17         3.42        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 
        0.56        16.31        15.58         7.40        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 
        3.32        11.80        19.17        15.85         3.72        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        0.46        11.57         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8532 
        0.30         0.07         0.07         0.07         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.10        11.31         0.10        12.62        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-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 
       29.98        19.07        12.03         0.00         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        12.66        19.13        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       17.85        13.35        15.98        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.44         9.76         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.40         7.13        14.47        21.27        11.38        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HU-8238 
       22.29        17.06        59.54         5.03         0.23         1.51 
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-A4GJ TCGA-HU-A4GN 
        5.59        12.30        11.84        24.20        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10        10.19         0.26         2.10        19.36        23.84 
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-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V 
        5.36        13.08        12.59         6.51         5.56         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73         9.86        45.67         8.52        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        9.24        11.05         5.13        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
        0.92        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       27.35        11.70        11.93        61.22        22.68         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50        52.24         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        5.72        21.04         2.66        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        10.62         0.79 

  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                       12.590                        12.805 
[1] "0.1 - 122.3 (12.6)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q21.3) MUTATED         7        8       19        9        29
  AMP PEAK  3(1Q21.3) WILD-TYPE       4       11       29       23        48
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q21.3) MUTATED          33        13         38         24
  AMP PEAK  3(1Q21.3) WILD-TYPE        51        16         59         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q21.3) MUTATED           15       21         4
  AMP PEAK  3(1Q21.3) WILD-TYPE         33       30         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  STAGE I                              7                             4
  STAGE IA                             8                            11
  STAGE IB                            19                            29
  STAGE II                             9                            23
  STAGE IIA                           29                            48
  STAGE IIB                           33                            51
  STAGE III                           13                            16
  STAGE IIIA                          38                            59
  STAGE IIIB                          24                            48
  STAGE IIIC                          15                            33
  STAGE IV                            21                            30
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  3(1Q21.3) MUTATED      29  47 113  38
  AMP PEAK  3(1Q21.3) WILD-TYPE    24  79 167  86
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  T0+T1                          29                            24
  T2                             47                            79
  T3                            113                           167
  T4                             38                            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  3(1Q21.3) MUTATED    80  68  34  37
  AMP PEAK  3(1Q21.3) WILD-TYPE 120 114  62  60
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  N0                          80                           120
  N1                          68                           114
  N2                          34                            62
  N3                          37                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   194  17
  AMP PEAK  3(1Q21.3) WILD-TYPE 319  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    194   17
  AMP PEAK  3(1Q21.3) WILD-TYPE  319   22
   clus
vv  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  0                         194                           319
  1                          17                            22
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED    63 175
  AMP PEAK  3(1Q21.3) WILD-TYPE 119 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED     63  175
  AMP PEAK  3(1Q21.3) WILD-TYPE  119  252
        clus
vv       AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  FEMALE                          63                           119
  MALE                           175                           252
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  3(1Q21.3) MUTATED                                      16
  AMP PEAK  3(1Q21.3) WILD-TYPE                                    55
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q21.3) MUTATED                                                       59
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(1Q21.3) MUTATED                                                                  32
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                                49
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  3(1Q21.3) MUTATED                                                 33
  AMP PEAK  3(1Q21.3) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  3(1Q21.3) MUTATED                                                          6
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  3(1Q21.3) MUTATED                                                           4
  AMP PEAK  3(1Q21.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  3(1Q21.3) MUTATED                                          6
  AMP PEAK  3(1Q21.3) WILD-TYPE                                        7
D3V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  3(1Q21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  AMP PEAK  3(1Q21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED     5 233
  AMP PEAK  3(1Q21.3) WILD-TYPE   1 370
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED      5  233
  AMP PEAK  3(1Q21.3) WILD-TYPE    1  370
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  NO                            5                             1
  YES                         233                           370
[1] 2 2
[1] FALSE
D3V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q21.3) MUTATED   118  10   9   9
  AMP PEAK  3(1Q21.3) WILD-TYPE 229   8  10  16
D3V11, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  R0                         118                           229
  R1                          10                             8
  R2                           9                            10
  RX                           9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q21.3) MUTATED      56                         6
  AMP PEAK  3(1Q21.3) WILD-TYPE    73                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q21.3) MUTATED                                           1   145
  AMP PEAK  3(1Q21.3) WILD-TYPE                                         0   240
D3V13, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q21.3) MUTATED
  ASIAN                                                              56
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             145
                                           clus
vv                                          AMP PEAK  3(1Q21.3) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED     1 157
  AMP PEAK  3(1Q21.3) WILD-TYPE   6 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED      1  157
  AMP PEAK  3(1Q21.3) WILD-TYPE    6  237
                        clus
vv                       AMP PEAK  3(1Q21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         157
                        clus
vv                       AMP PEAK  3(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           237
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(1Q42.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(1Q42.3) MUTATED   131  90
  AMP PEAK  4(1Q42.3) WILD-TYPE 223 131
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          221                           354 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                           90                           131 
$`AMP PEAK  4(1Q42.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE 
       25.78        31.27        13.94         8.94        16.24         7.69 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       20.09         0.85         2.63        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03         0.79        23.41        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
      122.10        60.39         3.68        42.77        31.56        25.22 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30         3.68        32.61        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        1.38         4.90         7.43         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL 
        3.95         3.02        55.50         2.66        12.92        13.22 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        5.49        52.57        46.09        10.36         5.92        10.45 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35         0.10        13.25        12.49        12.76 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.00        12.23        13.18         0.13         5.06        14.70 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
       29.59         6.35        53.95        15.78        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
        3.42         4.80         9.27         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       42.87        46.19        15.91        10.16         2.10        19.73 
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
       11.01         6.61         6.18        19.33         9.17        25.61 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8059 
        9.21        15.42        28.01        18.15        28.73        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       11.44         0.69         9.60        12.95         2.66         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 
        7.40         6.18        19.50        14.04         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 
        8.22         7.53        22.26         0.72        12.82        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
        0.46        20.42         1.15        13.15         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
        0.10         0.16         0.13         3.42         9.34        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 
        6.58        12.20         7.99        54.08        19.07        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-5578 
       18.97         7.07        12.00         1.02         4.01        12.66 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       11.93        18.84        18.54        17.19        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU 
       10.55        11.31        12.33        24.72        19.50        16.44 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       11.31         2.96         0.62         7.99        16.24        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        3.48        14.07         0.56         5.52        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC 
        5.92        14.27        12.59        14.17         0.76         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 
       22.75        25.81        11.77         0.10         6.51        12.95 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42         3.45         5.19        13.08         1.41         6.44 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 
        7.82        60.56        18.21         6.08       122.30       115.69 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PY 
       35.24         7.73        12.79         2.70        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y 
       65.16        36.69        18.74        20.81        22.68         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       52.24         9.04         4.54        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6K 
       11.24        18.41        32.94        17.13        12.43 

$`AMP PEAK  4(1Q42.3) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR 
       14.30        58.55         7.63         5.92         4.21        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A6QS 
        6.21        33.27        20.78         3.88         9.30         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 
       14.86        12.16        44.75        68.02        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        24.03         6.28         3.16        30.25 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        19.99        21.01 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.32         3.16        58.59        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        8.71        25.12        35.97        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76        21.37         8.71        13.41        27.12        83.24 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.41         0.10         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.59        12.59        22.39         0.10        25.25        10.52 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        7.04         9.30         2.89         1.45         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        5.29        15.35         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B 
       12.43         1.55        18.31        30.71        15.06        11.24 
TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.17         3.42         2.66        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       17.29        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 
       32.94        12.82        24.76        35.24        23.93        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
       12.26        20.55         8.05         0.56        16.31        15.58 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31         3.32        11.80        19.17        14.79        15.85 
TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        3.72        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.49        11.54        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56        13.87         6.08         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        19.36 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.18         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.10         0.13         0.10        11.31        12.43 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         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 
       36.00         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        69.04        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        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       15.65         8.38         4.34         7.40         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38        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        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        21.21        18.81         3.39        18.38         5.36 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         1.81        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
        9.86        45.67         8.52        61.25         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       27.35        64.57        11.70        11.93        61.22         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       36.16         7.36         9.50         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        5.72         2.66        22.09        40.08        28.41        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        21.11        10.62         0.79 

  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                       12.660                        12.985 
[1] "0.1 - 122.3 (12.7)" "0.0 - 116.4 (13.0)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(1Q42.3) MUTATED         5        9       18       10        29
  AMP PEAK  4(1Q42.3) WILD-TYPE       6       10       30       22        48
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(1Q42.3) MUTATED          27        14         38         25
  AMP PEAK  4(1Q42.3) WILD-TYPE        57        15         59         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(1Q42.3) MUTATED           19       19         4
  AMP PEAK  4(1Q42.3) WILD-TYPE         29       32         0
D4V3, multiclass
            clus
vv           AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  STAGE I                              5                             6
  STAGE IA                             9                            10
  STAGE IB                            18                            30
  STAGE II                            10                            22
  STAGE IIA                           29                            48
  STAGE IIB                           27                            57
  STAGE III                           14                            15
  STAGE IIIA                          38                            59
  STAGE IIIB                          25                            47
  STAGE IIIC                          19                            29
  STAGE IV                            19                            32
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  4(1Q42.3) MUTATED      30  44 104  45
  AMP PEAK  4(1Q42.3) WILD-TYPE    23  82 176  79
D4V4, multiclass
       clus
vv      AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  T0+T1                          30                            23
  T2                             44                            82
  T3                            104                           176
  T4                             45                            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  4(1Q42.3) MUTATED    75  71  35  36
  AMP PEAK  4(1Q42.3) WILD-TYPE 125 111  61  61
D4V5, multiclass
    clus
vv   AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  N0                          75                           125
  N1                          71                           111
  N2                          35                            61
  N3                          36                            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"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED   191  16
  AMP PEAK  4(1Q42.3) WILD-TYPE 322  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED    191   16
  AMP PEAK  4(1Q42.3) WILD-TYPE  322   23
   clus
vv  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  0                         191                           322
  1                          16                            23
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED    57 177
  AMP PEAK  4(1Q42.3) WILD-TYPE 125 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED     57  177
  AMP PEAK  4(1Q42.3) WILD-TYPE  125  250
        clus
vv       AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  FEMALE                          57                           125
  MALE                           177                           250
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  4(1Q42.3) MUTATED                                      12
  AMP PEAK  4(1Q42.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(1Q42.3) MUTATED                                                       53
  AMP PEAK  4(1Q42.3) WILD-TYPE                                                    109
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(1Q42.3) MUTATED                                                                  29
  AMP PEAK  4(1Q42.3) WILD-TYPE                                                                52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  4(1Q42.3) MUTATED                                                 39
  AMP PEAK  4(1Q42.3) WILD-TYPE                                               39
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  4(1Q42.3) MUTATED                                                          7
  AMP PEAK  4(1Q42.3) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  4(1Q42.3) MUTATED                                                           3
  AMP PEAK  4(1Q42.3) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  4(1Q42.3) MUTATED                                          5
  AMP PEAK  4(1Q42.3) WILD-TYPE                                        8
D4V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  4(1Q42.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK  4(1Q42.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED     3 231
  AMP PEAK  4(1Q42.3) WILD-TYPE   3 372
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED      3  231
  AMP PEAK  4(1Q42.3) WILD-TYPE    3  372
     clus
vv    AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  NO                            3                             3
  YES                         231                           372
[1] 2 2
[1] FALSE
D4V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(1Q42.3) MUTATED   115   8   7   9
  AMP PEAK  4(1Q42.3) WILD-TYPE 232  10  12  16
D4V11, multiclass
    clus
vv   AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  R0                         115                           232
  R1                           8                            10
  R2                           7                            12
  RX                           9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(1Q42.3) MUTATED      57                         8
  AMP PEAK  4(1Q42.3) WILD-TYPE    72                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(1Q42.3) MUTATED                                           0   143
  AMP PEAK  4(1Q42.3) WILD-TYPE                                         1   242
D4V13, multiclass
                                           clus
vv                                          AMP PEAK  4(1Q42.3) MUTATED
  ASIAN                                                              57
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             143
                                           clus
vv                                          AMP PEAK  4(1Q42.3) WILD-TYPE
  ASIAN                                                                72
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED     1 153
  AMP PEAK  4(1Q42.3) WILD-TYPE   6 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED      1  153
  AMP PEAK  4(1Q42.3) WILD-TYPE    6  241
                        clus
vv                       AMP PEAK  4(1Q42.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         153
                        clus
vv                       AMP PEAK  4(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           241
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(2Q12.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(2Q12.2) MUTATED    86  54
  AMP PEAK  5(2Q12.2) WILD-TYPE 268 167
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          140                           435 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                           54                           167 
$`AMP PEAK  5(2Q12.2) MUTATED`
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A5S3 
       13.94         8.94        16.24         6.21        20.09        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J 
       14.50        44.75        31.56        25.22         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        8.94        32.61        47.93         3.32         1.38         3.16 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NR 
        7.13         7.43         2.60         3.95        55.50         8.71 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
       52.57         5.92         0.10        13.15        13.25         0.10 
TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       12.49         0.10        12.33        25.25        12.00        12.03 
TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW 
        7.04        29.59         6.35        53.95        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EX 
        3.42         4.80        15.35        18.81        19.96        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       30.71        46.19        10.16         3.42         2.10         2.66 
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
       11.01         6.61        18.35        17.29        19.33         9.17 
TCGA-BR-6566 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       32.78        12.82         9.21        35.24        15.42        18.15 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 
        0.69         9.60         2.20        13.08         5.39         9.21 
TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-A486 
        1.48        13.51        20.42        13.18         0.07         3.42 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5727 
       12.43        11.61        47.05        21.99        36.00        79.07 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-A4YU TCGA-D7-A6EV 
       18.54        17.19        10.26        15.22        16.44        11.24 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
        7.99        72.23         3.48        19.53        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
        5.52         5.92        14.17         0.76        24.30        12.30 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        11.77         8.98         6.25         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS 
       23.84        12.30         3.45         5.36        13.08        12.59 
TCGA-IN-A7NT TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7C1 TCGA-VQ-A8DU 
        5.56        37.64         9.86        45.67        16.67         5.46 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q 
       35.24         7.73        22.19        12.79        17.85        20.81 
TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J 
        1.71        64.18        40.08        29.98        54.12        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`AMP PEAK  5(2Q12.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        2.63        20.12        18.64         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI 
        3.16        30.25        24.00         3.68         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       21.01        18.35         7.17        58.59         4.90        29.00 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        6.94         8.71        25.12         0.36         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.66        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       83.24        46.09        10.36        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.41        15.35         0.10        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        10.52        12.23        13.18        33.11         5.16 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         2.89         1.45         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        5.29         9.27         4.44        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31         8.12        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.17        15.91        19.73        26.70        11.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.97         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        26.10        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93        28.01        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         9.34        11.31         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-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-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        14.27         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-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        16.24        14.47        21.27        11.38 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       12.10        10.62         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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        19.36         9.67         8.88         8.81        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-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.44         6.74         6.51         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       28.96        34.29        46.26        16.31         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        18.74        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        22.09        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       26.04        16.14        12.43 

  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                        79.07                        122.30 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                        12.46                         12.82 
[1] "0.1 - 79.1 (12.5)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(2Q12.2) MUTATED         1        8       12        7        21
  AMP PEAK  5(2Q12.2) WILD-TYPE      10       11       36       25        56
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(2Q12.2) MUTATED          27         8         16         12
  AMP PEAK  5(2Q12.2) WILD-TYPE        57        21         81         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q12.2) MUTATED           12        6         2
  AMP PEAK  5(2Q12.2) WILD-TYPE         36       45         2
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  STAGE I                              1                            10
  STAGE IA                             8                            11
  STAGE IB                            12                            36
  STAGE II                             7                            25
  STAGE IIA                           21                            56
  STAGE IIB                           27                            57
  STAGE III                            8                            21
  STAGE IIIA                          16                            81
  STAGE IIIB                          12                            60
  STAGE IIIC                          12                            36
  STAGE IV                             6                            45
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  5(2Q12.2) MUTATED      15  29  75  17
  AMP PEAK  5(2Q12.2) WILD-TYPE    38  97 205 107
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  T0+T1                          15                            38
  T2                             29                            97
  T3                             75                           205
  T4                             17                           107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  5(2Q12.2) MUTATED    52  43  18  21
  AMP PEAK  5(2Q12.2) WILD-TYPE 148 139  78  76
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  N0                          52                           148
  N1                          43                           139
  N2                          18                            78
  N3                          21                            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"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED   115   7
  AMP PEAK  5(2Q12.2) WILD-TYPE 398  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED    115    7
  AMP PEAK  5(2Q12.2) WILD-TYPE  398   32
   clus
vv  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  0                         115                           398
  1                           7                            32
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED    37 111
  AMP PEAK  5(2Q12.2) WILD-TYPE 145 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED     37  111
  AMP PEAK  5(2Q12.2) WILD-TYPE  145  316
        clus
vv       AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  FEMALE                          37                           145
  MALE                           111                           316
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  5(2Q12.2) MUTATED                                      10
  AMP PEAK  5(2Q12.2) WILD-TYPE                                    61
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(2Q12.2) MUTATED                                                       33
  AMP PEAK  5(2Q12.2) WILD-TYPE                                                    129
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(2Q12.2) MUTATED                                                                  17
  AMP PEAK  5(2Q12.2) WILD-TYPE                                                                64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  5(2Q12.2) MUTATED                                                 20
  AMP PEAK  5(2Q12.2) WILD-TYPE                                               58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  5(2Q12.2) MUTATED                                                          2
  AMP PEAK  5(2Q12.2) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  5(2Q12.2) MUTATED                                                           3
  AMP PEAK  5(2Q12.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  5(2Q12.2) MUTATED                                          1
  AMP PEAK  5(2Q12.2) WILD-TYPE                                       12
D5V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  5(2Q12.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    1
                                                                   clus
vv                                                                  AMP PEAK  5(2Q12.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED     0 148
  AMP PEAK  5(2Q12.2) WILD-TYPE   6 455
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED      0  148
  AMP PEAK  5(2Q12.2) WILD-TYPE    6  455
     clus
vv    AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  NO                            0                             6
  YES                         148                           455
[1] 2 2
[1] FALSE
D5V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(2Q12.2) MUTATED    71   2   2   4
  AMP PEAK  5(2Q12.2) WILD-TYPE 276  16  17  21
D5V11, multiclass
    clus
vv   AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  R0                          71                           276
  R1                           2                            16
  R2                           2                            17
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(2Q12.2) MUTATED      37                         5
  AMP PEAK  5(2Q12.2) WILD-TYPE    92                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(2Q12.2) MUTATED                                           0    92
  AMP PEAK  5(2Q12.2) WILD-TYPE                                         1   293
D5V13, multiclass
                                           clus
vv                                          AMP PEAK  5(2Q12.2) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              92
                                           clus
vv                                          AMP PEAK  5(2Q12.2) WILD-TYPE
  ASIAN                                                                92
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED     2  99
  AMP PEAK  5(2Q12.2) WILD-TYPE   5 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED      2   99
  AMP PEAK  5(2Q12.2) WILD-TYPE    5  295
                        clus
vv                       AMP PEAK  5(2Q12.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       AMP PEAK  5(2Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           295
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(3Q26.2) MUTATED   159 104
  AMP PEAK  6(3Q26.2) WILD-TYPE 195 117
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          263                           312 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          104                           117 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        60.39         3.68 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       42.77        23.18        25.22        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       24.00        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z 
        3.16        29.00         7.13         6.94         2.60         7.40 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
       55.50         2.66        35.97        16.47        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        27.12        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.25        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.23        12.03        13.18         0.13         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.59         5.06         6.35        53.95         2.89        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         3.42         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6456 
        9.44         6.61        18.35         6.18        34.68        17.29 
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 TCGA-BR-7723 
        9.17        21.11        30.90        12.82        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8289 
        3.45        12.76        14.43        11.44         8.05         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 
        2.20        15.58        19.50        26.33        14.79        25.18 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ 
       12.79        15.81         7.53         8.22         7.53        22.26 
TCGA-BR-A4IU TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       13.41         0.53        19.36        20.65        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        3.25        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.16         0.13         9.34        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4444 
       12.20         3.02        15.95         7.99         8.05        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 
       19.07        12.03         0.00        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         3.48        14.07        22.29        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G6 TCGA-HU-A4G9 
        0.56         0.23        26.47         5.92        12.30        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 
        3.25        22.75        25.81        11.77         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RL 
       12.95        19.36        23.84         9.67        27.42         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 
       13.08         1.41         6.44         5.56         1.81        60.56 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
       45.67        18.21         6.08        16.67       115.69        35.61 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP 
       21.73         7.73        16.31         2.70        17.85        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q 
       13.35        27.35        64.57        65.16        11.93        20.81 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 
        9.73        52.24         9.04         2.01         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       64.18        21.04        42.54        18.41        40.08        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       29.98        54.12        21.11        12.43         0.79 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6F8 
       25.78        13.94         8.94         9.30        14.86       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
       68.02        41.52        25.41        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        6.28         3.16         8.94         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T 
       19.99        21.01        58.59         4.90         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36         3.95         3.02        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49U 
       13.55         7.76        21.37        83.24        46.09        15.35 
TCGA-LN-A49X TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.10        33.11         7.82        14.70         7.04        29.59 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
        9.30        15.78         1.45         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE 
        4.80        15.35         1.55        46.19        10.16         2.10 
TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        2.66         9.47         6.97         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        9.57         6.61        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 
       12.16         8.98        31.20        32.94         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 
       35.24        23.93        15.42        28.01        18.15        12.43 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        9.07        18.71        17.49         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 
       20.55         0.56        12.95        16.31         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8368 
       13.08         0.26        22.19        17.52         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 
        3.72         5.39         9.21        20.22         1.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         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-A453 
        9.86        15.68        10.68        12.56        13.87         6.08 
TCGA-BR-A4CS TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL 
       12.82         0.66        13.51         0.46         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8529 
        5.13         2.83        13.15         0.30         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         3.42        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 
        6.58         0.10        12.62        20.02        27.02         1.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 
       54.08         4.01        14.01        29.98        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       18.97         7.07        22.98         6.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        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        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        14.27         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.31        11.44        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.40         7.13         7.99        14.47        72.23        11.38 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB 
       19.53        17.06        59.54         5.03         5.52        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ 
       10.62         0.76        24.30         5.59        11.84        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-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38         5.36         6.74        12.59         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         2.53         5.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73         9.86         8.52        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04         5.79        13.25        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A 
        1.87         9.27        15.65        26.24        14.33        36.69 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94T 
        7.36         9.50        55.43         6.58         2.66        11.24 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       22.09        28.41        17.13        26.04        16.14        10.62 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         0.00                          0.07 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       115.69                        122.30 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       12.760                        12.725 
[1] "0.0 - 115.7 (12.8)" "0.1 - 122.3 (12.7)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(3Q26.2) MUTATED         3        9       17       12        38
  AMP PEAK  6(3Q26.2) WILD-TYPE       8       10       31       20        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(3Q26.2) MUTATED          41        23         40         28
  AMP PEAK  6(3Q26.2) WILD-TYPE        43         6         57         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.2) MUTATED           27       20         3
  AMP PEAK  6(3Q26.2) WILD-TYPE         21       31         1
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             9                            10
  STAGE IB                            17                            31
  STAGE II                            12                            20
  STAGE IIA                           38                            39
  STAGE IIB                           41                            43
  STAGE III                           23                             6
  STAGE IIIA                          40                            57
  STAGE IIIB                          28                            44
  STAGE IIIC                          27                            21
  STAGE IV                            20                            31
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  6(3Q26.2) MUTATED      23  56 126  57
  AMP PEAK  6(3Q26.2) WILD-TYPE    30  70 154  67
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  T0+T1                          23                            30
  T2                             56                            70
  T3                            126                           154
  T4                             57                            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  6(3Q26.2) MUTATED    88  88  40  42
  AMP PEAK  6(3Q26.2) WILD-TYPE 112  94  56  55
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  N0                          88                           112
  N1                          88                            94
  N2                          40                            56
  N3                          42                            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"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED   227  16
  AMP PEAK  6(3Q26.2) WILD-TYPE 286  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED    227   16
  AMP PEAK  6(3Q26.2) WILD-TYPE  286   23
   clus
vv  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  0                         227                           286
  1                          16                            23
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED    71 205
  AMP PEAK  6(3Q26.2) WILD-TYPE 111 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     71  205
  AMP PEAK  6(3Q26.2) WILD-TYPE  111  222
        clus
vv       AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  FEMALE                          71                           111
  MALE                           205                           222
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  6(3Q26.2) MUTATED                                      20
  AMP PEAK  6(3Q26.2) WILD-TYPE                                    51
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(3Q26.2) MUTATED                                                       59
  AMP PEAK  6(3Q26.2) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(3Q26.2) MUTATED                                                                  33
  AMP PEAK  6(3Q26.2) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  6(3Q26.2) MUTATED                                                 32
  AMP PEAK  6(3Q26.2) WILD-TYPE                                               46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  6(3Q26.2) MUTATED                                                          6
  AMP PEAK  6(3Q26.2) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  6(3Q26.2) MUTATED                                                           2
  AMP PEAK  6(3Q26.2) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  6(3Q26.2) MUTATED                                          5
  AMP PEAK  6(3Q26.2) WILD-TYPE                                        8
D6V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  6(3Q26.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK  6(3Q26.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     2 274
  AMP PEAK  6(3Q26.2) WILD-TYPE   4 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      2  274
  AMP PEAK  6(3Q26.2) WILD-TYPE    4  329
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  NO                            2                             4
  YES                         274                           329
[1] 2 2
[1] FALSE
D6V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(3Q26.2) MUTATED   123   6   8   9
  AMP PEAK  6(3Q26.2) WILD-TYPE 224  12  11  16
D6V11, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  R0                         123                           224
  R1                           6                            12
  R2                           8                            11
  RX                           9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(3Q26.2) MUTATED      74                         7
  AMP PEAK  6(3Q26.2) WILD-TYPE    55                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(3Q26.2) MUTATED                                           0   159
  AMP PEAK  6(3Q26.2) WILD-TYPE                                         1   226
D6V13, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q26.2) MUTATED
  ASIAN                                                              74
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             159
                                           clus
vv                                          AMP PEAK  6(3Q26.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     4 167
  AMP PEAK  6(3Q26.2) WILD-TYPE   3 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      4  167
  AMP PEAK  6(3Q26.2) WILD-TYPE    3  227
                        clus
vv                       AMP PEAK  6(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         167
                        clus
vv                       AMP PEAK  6(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           227
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P15.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(5P15.33) MUTATED   132  76
  AMP PEAK  7(5P15.33) WILD-TYPE 222 145
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           208                            367 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            76                            145 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A3YC 
       14.30         5.92        32.45        33.27         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
       18.64         0.53         0.79        23.41         4.67        14.50 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
       44.75        68.02         3.68        42.77        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI 
        3.16         0.30         4.31         8.94        32.61        19.99 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       47.93         7.17         3.16         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG 
        6.94         2.60         0.36         3.95        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       12.92        16.47        13.55        13.41        27.12        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36         5.92        13.41         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25         0.10        12.46        12.59        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.16         5.06        14.70        29.59        53.95        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00        20.38         3.42         4.80        18.81        19.96 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I 
       18.31        30.71        18.18        42.87        15.06        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-7197 
        3.42         2.10         2.66        19.73         4.64         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 
       35.24        15.42        28.01        18.15         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 
        0.69         8.05        12.95         2.66        15.58         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       17.52        26.33        14.79         9.21        20.22        11.54 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 
        8.22        20.65        13.64        13.15        13.18         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A 
        0.10         0.13         0.13         0.13         3.42        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 
       11.61        12.20         7.99        54.08        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 
       12.03        18.97         7.07        12.00        22.98        36.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5578 
        0.99        12.03        15.02         4.01        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       11.93        19.13        17.19        10.26        15.22        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.31        24.72        14.66        11.31         2.96        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.40         0.62         7.99        72.23         3.48        19.53 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G2 
       17.06         0.23         1.51        12.59        14.17        24.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
        3.25        22.75        25.81        11.77         6.25         2.10 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT 
       12.30        27.42         3.45         5.19         6.74         5.56 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV 
        5.56        20.15        45.67        18.21         8.61       122.30 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        35.61         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91A 
       18.48        35.24        21.73        12.79        17.85        36.69 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       18.74         1.71        36.16         9.50        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54         6.58        11.24        18.41        40.08        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       54.12        16.14        21.11         0.79 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 
       14.86        12.16       122.10        60.39        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE 
       21.70        23.18        24.03         6.28        30.25        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        3.68         4.70        21.01        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       58.59         7.43         8.71        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        13.48        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        8.71        83.24        46.09        10.45        12.66        12.43 
TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A9FO TCGA-M9-A5M8 
        0.10        12.49        12.76        11.54         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.82         8.02         7.59         7.04         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
        2.89         1.45        12.69        20.02         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         4.44        22.82        12.43         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-B7-5816 
       28.11        46.19        11.24         9.17        10.16        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
       31.20        32.94        12.82        24.76        23.93        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 
       14.43        12.26         9.60        20.55         0.56        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 
        2.20         7.40         6.18        19.50        13.08        22.19 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 
        0.26        15.85         3.72         5.39        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.49        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.07         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
        0.10         0.10         0.10         9.34        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        1.02         8.05         4.01        29.98        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        0.00         9.01        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
        6.02       105.07        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       21.07         7.99        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8572 
       17.85        13.35        15.98        12.79        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-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-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76         8.38         4.34         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
       16.24        14.47        21.27        11.38        14.07        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         5.52        18.08 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47         5.92        14.27        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76         5.59        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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.21        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        1.41         6.44        12.59         6.51         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        60.56        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         5.13        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
      116.38        71.38        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       48.79        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       34.29        46.26        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        20.81        22.68         7.36         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         5.72        64.18        21.04         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       22.09        28.41        29.98        17.13        26.04        12.43 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                         122.3                          122.1 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        12.855                         12.760 
[1] "0.1 - 122.3 (12.9)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1.1"
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(5P15.33) MUTATED         1        6       16       11        35
  AMP PEAK  7(5P15.33) WILD-TYPE      10       13       32       21        42
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(5P15.33) MUTATED          26        14         39         20
  AMP PEAK  7(5P15.33) WILD-TYPE        58        15         58         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  7(5P15.33) MUTATED           15       19         1
  AMP PEAK  7(5P15.33) WILD-TYPE         33       32         3
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              6                             13
  STAGE IB                             16                             32
  STAGE II                             11                             21
  STAGE IIA                            35                             42
  STAGE IIB                            26                             58
  STAGE III                            14                             15
  STAGE IIIA                           39                             58
  STAGE IIIB                           20                             52
  STAGE IIIC                           15                             33
  STAGE IV                             19                             32
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK  7(5P15.33) MUTATED      11  48 123  26
  AMP PEAK  7(5P15.33) WILD-TYPE    42  78 157  98
D7V4, multiclass
       clus
vv      AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  T0+T1                           11                             42
  T2                              48                             78
  T3                             123                            157
  T4                              26                             98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  7(5P15.33) MUTATED    75  65  34  32
  AMP PEAK  7(5P15.33) WILD-TYPE 125 117  62  65
D7V5, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  N0                           75                            125
  N1                           65                            117
  N2                           34                             62
  N3                           32                             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"
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   179  14
  AMP PEAK  7(5P15.33) WILD-TYPE 334  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    179   14
  AMP PEAK  7(5P15.33) WILD-TYPE  334   25
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                          179                            334
  1                           14                             25
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED    54 163
  AMP PEAK  7(5P15.33) WILD-TYPE 128 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     54  163
  AMP PEAK  7(5P15.33) WILD-TYPE  128  264
        clus
vv       AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  FEMALE                           54                            128
  MALE                            163                            264
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  7(5P15.33) MUTATED                                      12
  AMP PEAK  7(5P15.33) WILD-TYPE                                    59
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P15.33) MUTATED                                                       40
  AMP PEAK  7(5P15.33) WILD-TYPE                                                    122
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P15.33) MUTATED                                                                  31
  AMP PEAK  7(5P15.33) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  7(5P15.33) MUTATED                                                 28
  AMP PEAK  7(5P15.33) WILD-TYPE                                               50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  7(5P15.33) MUTATED                                                          8
  AMP PEAK  7(5P15.33) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  7(5P15.33) MUTATED                                                           4
  AMP PEAK  7(5P15.33) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  7(5P15.33) MUTATED                                          3
  AMP PEAK  7(5P15.33) WILD-TYPE                                       10
D7V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  7(5P15.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK  7(5P15.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     2 215
  AMP PEAK  7(5P15.33) WILD-TYPE   4 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      2  215
  AMP PEAK  7(5P15.33) WILD-TYPE    4  388
     clus
vv    AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  NO                             2                              4
  YES                          215                            388
[1] 2 2
[1] FALSE
D7V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(5P15.33) MUTATED   102   6   7   5
  AMP PEAK  7(5P15.33) WILD-TYPE 245  12  12  20
D7V11, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  R0                          102                            245
  R1                            6                             12
  R2                            7                             12
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(5P15.33) MUTATED      56                         6
  AMP PEAK  7(5P15.33) WILD-TYPE    73                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  7(5P15.33) MUTATED                                           1
  AMP PEAK  7(5P15.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK  7(5P15.33) MUTATED     129
  AMP PEAK  7(5P15.33) WILD-TYPE   256
D7V13, multiclass
                                           clus
vv                                          AMP PEAK  7(5P15.33) MUTATED
  ASIAN                                                               56
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              129
                                           clus
vv                                          AMP PEAK  7(5P15.33) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     1 133
  AMP PEAK  7(5P15.33) WILD-TYPE   6 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      1  133
  AMP PEAK  7(5P15.33) WILD-TYPE    6  261
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(5P13.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(5P13.1) MUTATED   122  73
  AMP PEAK  8(5P13.1) WILD-TYPE 232 148
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          195                           380 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                           73                           148 
$`AMP PEAK  8(5P13.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 
       14.30         5.92        16.24        32.45        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12        18.64         0.53         0.79        23.41 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        4.67        14.50        44.75        68.02         3.68        42.77 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OH 
       31.56        25.22         3.16         4.31         8.94        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       19.99        47.93         7.17         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE 
        7.13         6.94         2.60         0.36         3.95        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT 
       35.97        12.92        13.55        21.37        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
       52.57        46.09        10.36        13.41         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
        0.10        12.59        12.59         0.10        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO 
       13.18         5.16         5.06        14.70        53.95         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY 
       20.38         3.42         4.44        19.96        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       42.87        15.06        15.91         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.73         4.64        19.33         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       28.01        18.15         3.45        18.71        11.44         0.69 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 
        8.05        12.95         2.66        15.58         0.26        17.52 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 
       26.33        14.04        14.79         9.21        20.22        11.54 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
        8.22        22.26        20.65        13.64        13.18         0.07 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.10         0.13         3.42        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       12.20         7.99        54.08        47.05        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 
       18.97         7.07        12.00        22.98        36.00         0.99 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       12.03        15.02         4.01        12.66        11.93        19.13 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 
       10.26        15.22        10.55        11.31        24.72        14.66 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       11.31         2.96        15.65         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 
        3.48        19.53        17.06         0.23         1.51        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       14.17        12.10        24.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL 
       11.77         2.10        12.30        27.42         3.45         5.19 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A93G 
        6.51         5.56         1.81         7.82         5.56        20.15 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU 
       45.67        18.21        57.44         8.94        35.61         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8PH TCGA-VQ-A8PK 
       13.25        13.02        18.48        21.73        12.79        17.85 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.69        18.74         9.50         9.73        52.24         9.04 
TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
        6.58        11.24        40.08        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`AMP PEAK  8(5P13.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
        4.21         7.69         6.21        20.09        20.78         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
        9.30        17.03        12.82         9.96        14.86        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39        41.52        25.41        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         6.28        30.25         0.30        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
        4.70        21.01        18.35         3.32         1.38        58.59 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
        7.43         8.71        25.12         7.40         3.02         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.22         7.76         5.49         8.71 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       83.24         5.92        10.45        12.66        12.43        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35         0.10        12.46        12.49        12.76        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW 
       15.52        11.54        10.52         0.13        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02         7.59         7.04        29.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45        12.69        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80        15.35         9.27        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55        18.31         8.12        18.18        46.19        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.17        10.16        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         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 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-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        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       17.49        14.43        12.26         9.60        20.55         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20         7.40         6.18        19.50        13.08 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       22.19         0.95         4.31         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 
        0.26        15.85         3.72         5.39        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.49        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-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-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       19.07         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99         6.02       105.07        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 
       69.04        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        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-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-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.40         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         5.52        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 
       23.84         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.39        18.38         5.36        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.74        12.59        13.51         2.53        60.56        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73         9.86         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E2 
       16.87        19.04         5.79         0.92        48.79        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       46.26        16.31        22.19         2.50         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        65.16        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 
       20.81        22.68         1.71        36.16         7.36         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        22.09        18.41        28.41        29.98        17.13 
TCGA-VQ-AA6G TCGA-ZA-A8F6 
       26.04        10.62 

  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                        72.23                        122.30 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                       12.660                        12.775 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(5P13.1) MUTATED         1        7       16       10        30
  AMP PEAK  8(5P13.1) WILD-TYPE      10       12       32       22        47
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(5P13.1) MUTATED          26        12         34         17
  AMP PEAK  8(5P13.1) WILD-TYPE        58        17         63         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P13.1) MUTATED           18       18         2
  AMP PEAK  8(5P13.1) WILD-TYPE         30       33         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  STAGE I                              1                            10
  STAGE IA                             7                            12
  STAGE IB                            16                            32
  STAGE II                            10                            22
  STAGE IIA                           30                            47
  STAGE IIB                           26                            58
  STAGE III                           12                            17
  STAGE IIIA                          34                            63
  STAGE IIIB                          17                            55
  STAGE IIIC                          18                            30
  STAGE IV                            18                            33
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  8(5P13.1) MUTATED      11  45 108  32
  AMP PEAK  8(5P13.1) WILD-TYPE    42  81 172  92
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  T0+T1                          11                            42
  T2                             45                            81
  T3                            108                           172
  T4                             32                            92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  8(5P13.1) MUTATED    68  65  26  35
  AMP PEAK  8(5P13.1) WILD-TYPE 132 117  70  62
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  N0                          68                           132
  N1                          65                           117
  N2                          26                            70
  N3                          35                            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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED   166  15
  AMP PEAK  8(5P13.1) WILD-TYPE 347  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED    166   15
  AMP PEAK  8(5P13.1) WILD-TYPE  347   24
   clus
vv  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  0                         166                           347
  1                          15                            24
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED    56 149
  AMP PEAK  8(5P13.1) WILD-TYPE 126 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED     56  149
  AMP PEAK  8(5P13.1) WILD-TYPE  126  278
        clus
vv       AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  FEMALE                          56                           126
  MALE                           149                           278
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  8(5P13.1) MUTATED                                      12
  AMP PEAK  8(5P13.1) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(5P13.1) MUTATED                                                       44
  AMP PEAK  8(5P13.1) WILD-TYPE                                                    118
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(5P13.1) MUTATED                                                                  28
  AMP PEAK  8(5P13.1) WILD-TYPE                                                                53
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  8(5P13.1) MUTATED                                                 24
  AMP PEAK  8(5P13.1) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  8(5P13.1) MUTATED                                                          8
  AMP PEAK  8(5P13.1) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  8(5P13.1) MUTATED                                                           3
  AMP PEAK  8(5P13.1) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  8(5P13.1) MUTATED                                          4
  AMP PEAK  8(5P13.1) WILD-TYPE                                        9
D8V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  8(5P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  AMP PEAK  8(5P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED     2 203
  AMP PEAK  8(5P13.1) WILD-TYPE   4 400
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED      2  203
  AMP PEAK  8(5P13.1) WILD-TYPE    4  400
     clus
vv    AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  NO                            2                             4
  YES                         203                           400
[1] 2 2
[1] FALSE
D8V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(5P13.1) MUTATED    98   7   7   5
  AMP PEAK  8(5P13.1) WILD-TYPE 249  11  12  20
D8V11, multiclass
    clus
vv   AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  R0                          98                           249
  R1                           7                            11
  R2                           7                            12
  RX                           5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(5P13.1) MUTATED      45                         6
  AMP PEAK  8(5P13.1) WILD-TYPE    84                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(5P13.1) MUTATED                                           0   127
  AMP PEAK  8(5P13.1) WILD-TYPE                                         1   258
D8V13, multiclass
                                           clus
vv                                          AMP PEAK  8(5P13.1) MUTATED
  ASIAN                                                              45
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             127
                                           clus
vv                                          AMP PEAK  8(5P13.1) WILD-TYPE
  ASIAN                                                                84
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED     1 124
  AMP PEAK  8(5P13.1) WILD-TYPE   6 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED      1  124
  AMP PEAK  8(5P13.1) WILD-TYPE    6  270
                        clus
vv                       AMP PEAK  8(5P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         124
                        clus
vv                       AMP PEAK  8(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(6P21.1) MUTATED    95  77
  AMP PEAK  9(6P21.1) WILD-TYPE 259 144
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          172                           403 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           77                           144 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       16.24         4.21         3.88         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OM 
       44.75        60.39        68.02        21.70        30.25        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S 
       18.35         7.17         1.38        58.59         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         0.36         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT 
       35.97        12.92        13.48         5.49        21.37        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V 
       52.57        10.36         5.92        10.45        13.15         0.10 
TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW 
        0.10        12.49        11.54        12.33        12.33        12.00 
TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.23         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASX 
       53.95        15.78         2.89        20.02         3.42         4.44 
TCGA-VR-A8EQ TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       22.82        15.91         2.10        11.01         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 
       18.35         6.18        17.29        13.68        19.33         9.17 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
        9.21        35.24        15.42        18.15        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 
       11.44        12.95         2.66        14.04        14.79        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A4CQ 
        9.21        20.22        11.54         9.86        15.68        22.26 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8535 
       20.65        20.42        13.64         3.25         0.07         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 
        3.42         9.34        11.61         7.99        54.08        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5727 TCGA-CG-5730 
       12.03        18.97        30.97        36.00        79.07         4.01 
TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       69.04        19.13        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6F0 
       11.31        12.33        14.66        14.27        16.44         2.96 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
       15.65         7.99         3.48        19.53        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H5 
        5.52         5.92        14.17        25.81        23.84        12.30 
TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        9.67         3.39        18.38         5.19        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 
        6.74        12.59         5.56         2.53        37.64        45.67 
TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU 
       18.21         8.61       122.30        37.91       115.69         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       13.02        18.48        35.24         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 
       17.85        27.35        22.68         1.71         9.50         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 
        4.54        64.18        21.04        42.54        18.41        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       29.98        17.13        26.04         0.79 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27         5.92        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        9.96        14.86        14.50         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR 
        4.70        32.61        19.99        21.01         3.32         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43         8.71        25.12         7.40 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         7.76         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       83.24        46.09        12.66        12.43        13.41         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35        13.25        12.46        12.59        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       22.39         0.10        15.52        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.82         5.06         6.35         9.30         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         4.80        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        10.16         3.42         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        28.01        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10        11.31        12.43         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 
        8.05         4.01        14.01        29.98        47.05        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        22.98         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96        65.10        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 
       17.85        13.35        17.19        12.79        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV 
       19.50        17.19        18.21        21.14        20.91         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        19.36         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP 
       27.42        21.21         3.45        18.81         5.36         6.44 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       40.64       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81        36.16         7.36         9.73        52.24         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
       55.43         6.58         5.72         2.66        11.24        22.09 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        32.94        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                        13.05                         12.66 
[1] "0.1 - 122.3 (13.1)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6P21.1) MUTATED         7        5       16       10        22
  AMP PEAK  9(6P21.1) WILD-TYPE       4       14       32       22        55
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6P21.1) MUTATED          26        12         29         18
  AMP PEAK  9(6P21.1) WILD-TYPE        58        17         68         54
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P21.1) MUTATED            8       13         3
  AMP PEAK  9(6P21.1) WILD-TYPE         40       38         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              7                             4
  STAGE IA                             5                            14
  STAGE IB                            16                            32
  STAGE II                            10                            22
  STAGE IIA                           22                            55
  STAGE IIB                           26                            58
  STAGE III                           12                            17
  STAGE IIIA                          29                            68
  STAGE IIIB                          18                            54
  STAGE IIIC                           8                            40
  STAGE IV                            13                            38
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  9(6P21.1) MUTATED      19  44  82  26
  AMP PEAK  9(6P21.1) WILD-TYPE    34  82 198  98
D9V4, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T0+T1                          19                            34
  T2                             44                            82
  T3                             82                           198
  T4                             26                            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  9(6P21.1) MUTATED    62  62  28  21
  AMP PEAK  9(6P21.1) WILD-TYPE 138 120  68  76
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                          62                           138
  N1                          62                           120
  N2                          28                            68
  N3                          21                            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"
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED   150   9
  AMP PEAK  9(6P21.1) WILD-TYPE 363  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED    150    9
  AMP PEAK  9(6P21.1) WILD-TYPE  363   30
   clus
vv  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  0                         150                           363
  1                           9                            30
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED    47 138
  AMP PEAK  9(6P21.1) WILD-TYPE 135 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     47  138
  AMP PEAK  9(6P21.1) WILD-TYPE  135  289
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                          47                           135
  MALE                           138                           289
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK  9(6P21.1) MUTATED                                       4
  AMP PEAK  9(6P21.1) WILD-TYPE                                    67
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6P21.1) MUTATED                                                       50
  AMP PEAK  9(6P21.1) WILD-TYPE                                                    112
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6P21.1) MUTATED                                                                  30
  AMP PEAK  9(6P21.1) WILD-TYPE                                                                51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK  9(6P21.1) MUTATED                                                 30
  AMP PEAK  9(6P21.1) WILD-TYPE                                               48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK  9(6P21.1) MUTATED                                                          3
  AMP PEAK  9(6P21.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK  9(6P21.1) MUTATED                                                           2
  AMP PEAK  9(6P21.1) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK  9(6P21.1) MUTATED                                          2
  AMP PEAK  9(6P21.1) WILD-TYPE                                       11
D9V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK  9(6P21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  AMP PEAK  9(6P21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      112
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED     3 182
  AMP PEAK  9(6P21.1) WILD-TYPE   3 421
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      3  182
  AMP PEAK  9(6P21.1) WILD-TYPE    3  421
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  NO                            3                             3
  YES                         182                           421
[1] 2 2
[1] FALSE
D9V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(6P21.1) MUTATED    94   4   5  10
  AMP PEAK  9(6P21.1) WILD-TYPE 253  14  14  15
D9V11, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  R0                          94                           253
  R1                           4                            14
  R2                           5                            14
  RX                          10                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6P21.1) MUTATED      33                         6
  AMP PEAK  9(6P21.1) WILD-TYPE    96                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6P21.1) MUTATED                                           1   120
  AMP PEAK  9(6P21.1) WILD-TYPE                                         0   265
D9V13, multiclass
                                           clus
vv                                          AMP PEAK  9(6P21.1) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             120
                                           clus
vv                                          AMP PEAK  9(6P21.1) WILD-TYPE
  ASIAN                                                                96
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED     1 112
  AMP PEAK  9(6P21.1) WILD-TYPE   6 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      1  112
  AMP PEAK  9(6P21.1) WILD-TYPE    6  282
                        clus
vv                       AMP PEAK  9(6P21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       AMP PEAK  9(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           282
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6Q12) MUTATION ANALYSIS
D10V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 10(6Q12) MUTATED    67  60
  AMP PEAK 10(6Q12) WILD-TYPE 287 161
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        127                         448 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                         60                         161 
$`AMP PEAK 10(6Q12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3Y9 
       25.78         7.63        13.94        16.24         4.21         0.85 
TCGA-IG-A4QS TCGA-IG-A97H TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-L5-A43E 
        3.88        14.50        60.39        68.02         3.68        30.25 
TCGA-L5-A43M TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        8.94        47.93        18.35         7.13         7.43         6.94 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN 
        3.95         3.02         2.66        12.92        13.48         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       21.37        27.12        52.57        10.36         5.92        10.45 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       13.15        13.25        11.54        12.33         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.00        12.23        33.11         8.02        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-VR-A8EQ 
       29.59        53.95        15.78         2.89        20.38        22.82 
TCGA-VR-A8EZ TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       18.18        15.91         2.10        11.01         6.61         6.97 
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.18        17.29        19.33         9.21        35.24        15.42 
TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 
       28.73        11.44        12.95         2.66        14.04        14.79 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4J1 TCGA-BR-A4J8 
       25.18         9.21        11.54        15.68         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8533 TCGA-CD-A486 
       20.65        20.42        13.64         3.25         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
        9.34        12.43         7.99        54.08         4.01        18.97 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 
       30.97         1.02         4.01        17.19        10.26        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 
       11.31        12.33        14.66        14.27         2.96         7.99 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H6 
        3.48        19.53         5.52        25.81         6.51         9.67 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-KB-A6F7 TCGA-KB-A93H 
        3.39        18.38         5.19         1.41        60.56        37.64 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV 
        9.86         8.61        37.91       115.69         8.94        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S 
       13.02         7.73        22.19         2.70        17.85        22.68 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B 
        1.71         9.50         9.04        42.54        40.08        29.98 
TCGA-VQ-AA6F 
       54.12 

$`AMP PEAK 10(6Q12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GR 
       31.27        14.30        58.55         5.92         8.94        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27        20.09        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
      122.10        44.75        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       19.99        21.01         3.32         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59         4.90        29.00         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK 
        0.36         7.40        55.50        35.97        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
       13.22         7.76         8.71        13.41        83.24        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        13.41         0.10        15.35         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       22.39         0.10        15.52        13.22        25.25        10.52 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03        13.18         0.13         5.16         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        5.06         6.35         9.30         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        10.16         3.42         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        18.35        30.90         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.87        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       23.93        28.01        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        19.17         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        0.46         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        1.02         8.05        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         0.00         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       22.98         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.22        15.98        12.79        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        18.21        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
        8.81        27.42        21.21         3.45        18.81         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53         5.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        18.74        20.81        36.16         7.36 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        52.24         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                       0.13                        0.00 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                     115.69                      122.30 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                      12.33                       12.79 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D10V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(6Q12) MUTATED         5        2       13        6        19
  AMP PEAK 10(6Q12) WILD-TYPE       6       17       35       26        58
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(6Q12) MUTATED          18        10         19         12
  AMP PEAK 10(6Q12) WILD-TYPE        66        19         78         60
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6Q12) MUTATED            6       13         3
  AMP PEAK 10(6Q12) WILD-TYPE         42       38         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  STAGE I                            5                           6
  STAGE IA                           2                          17
  STAGE IB                          13                          35
  STAGE II                           6                          26
  STAGE IIA                         19                          58
  STAGE IIB                         18                          66
  STAGE III                         10                          19
  STAGE IIIA                        19                          78
  STAGE IIIB                        12                          60
  STAGE IIIC                         6                          42
  STAGE IV                          13                          38
  STAGE IVA                          3                           1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 10(6Q12) MUTATED      12  29  67  21
  AMP PEAK 10(6Q12) WILD-TYPE    41  97 213 103
D10V4, multiclass
       clus
vv      AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  T0+T1                        12                          41
  T2                           29                          97
  T3                           67                         213
  T4                           21                         103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 10(6Q12) MUTATED    48  45  16  18
  AMP PEAK 10(6Q12) WILD-TYPE 152 137  80  79
D10V5, multiclass
    clus
vv   AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  N0                        48                         152
  N1                        45                         137
  N2                        16                          80
  N3                        18                          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"
D10V6, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED   110  11
  AMP PEAK 10(6Q12) WILD-TYPE 403  28
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED    110   11
  AMP PEAK 10(6Q12) WILD-TYPE  403   28
   clus
vv  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  0                       110                         403
  1                        11                          28
[1] 2 2
[1] FALSE
D10V7, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED    37 100
  AMP PEAK 10(6Q12) WILD-TYPE 145 327
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED     37  100
  AMP PEAK 10(6Q12) WILD-TYPE  145  327
        clus
vv       AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  FEMALE                        37                         145
  MALE                         100                         327
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 10(6Q12) MUTATED                                       4
  AMP PEAK 10(6Q12) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(6Q12) MUTATED                                                       36
  AMP PEAK 10(6Q12) WILD-TYPE                                                    126
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(6Q12) MUTATED                                                                  27
  AMP PEAK 10(6Q12) WILD-TYPE                                                                54
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 10(6Q12) MUTATED                                                 15
  AMP PEAK 10(6Q12) WILD-TYPE                                               63
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 10(6Q12) MUTATED                                                          1
  AMP PEAK 10(6Q12) WILD-TYPE                                                       20
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 10(6Q12) MUTATED                                                           1
  AMP PEAK 10(6Q12) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 10(6Q12) MUTATED                                          2
  AMP PEAK 10(6Q12) WILD-TYPE                                       11
D10V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 10(6Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  AMP PEAK 10(6Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED     2 135
  AMP PEAK 10(6Q12) WILD-TYPE   4 468
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED      2  135
  AMP PEAK 10(6Q12) WILD-TYPE    4  468
     clus
vv    AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  NO                          2                           4
  YES                       135                         468
[1] 2 2
[1] FALSE
D10V10, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 10(6Q12) MUTATED    65   3   5   8
  AMP PEAK 10(6Q12) WILD-TYPE 282  15  14  17
D10V11, multiclass
    clus
vv   AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  R0                        65                         282
  R1                         3                          15
  R2                         5                          14
  RX                         8                          17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(6Q12) MUTATED      26                         3
  AMP PEAK 10(6Q12) WILD-TYPE   103                        10
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(6Q12) MUTATED                                           1    86
  AMP PEAK 10(6Q12) WILD-TYPE                                         0   299
D10V13, multiclass
                                           clus
vv                                          AMP PEAK 10(6Q12) MUTATED
  ASIAN                                                            26
  BLACK OR AFRICAN AMERICAN                                         3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            86
                                           clus
vv                                          AMP PEAK 10(6Q12) WILD-TYPE
  ASIAN                                                             103
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             299
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED     0  82
  AMP PEAK 10(6Q12) WILD-TYPE   7 312
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED      0   82
  AMP PEAK 10(6Q12) WILD-TYPE    7  312
                        clus
vv                       AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           7
  NOT HISPANIC OR LATINO                        82                         312
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q21) MUTATED    53  49
  AMP PEAK 11(6Q21) WILD-TYPE 301 172
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        102                         473 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         49                         172 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IG-A4QS TCGA-JY-A6FD TCGA-L5-A43E 
       14.30         7.63        13.94         3.88        68.02        30.25 
TCGA-L5-A4OG TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        4.70         7.43         6.94         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L7-A6VZ 
        2.66        12.92        13.48        21.37        27.12        10.36 
TCGA-LN-A49L TCGA-LN-A5U5 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
       10.45         4.47         8.02        14.70         7.04        15.78 
TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7I TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       18.18        11.24        15.91        11.01         6.61         6.97 
TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8060 
       17.29         9.21        35.24        15.42        18.15        11.44 
TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 
        2.66        14.04        14.79        25.18         9.21        11.54 
TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J7 
       15.68         7.53        22.26         1.48         0.72        19.36 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 
        3.25        13.15         0.10         9.34        12.43         3.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4477 
        7.99        54.08         4.01        47.05        18.97        30.97 
TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 
       12.03        18.54        10.26        15.22        10.55        11.31 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-A4BF TCGA-HU-A4GH 
       12.33        14.27         7.99        16.24         5.52        11.77 
TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        6.51        12.95         9.67         3.45        18.81         3.39 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 
        1.81         5.56         9.86        45.67         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91         8.94         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U 
       35.24        22.19         2.70        17.85        22.68         1.71 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-VQ-AA6J 
        9.50         9.04        64.18        42.54        17.13        21.11 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH 
        0.30         4.31         8.94        24.00         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NG 
        8.71         2.60        25.12         0.36         7.40        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M 
       13.41        83.24        52.57        46.09         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        29.59         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       26.70        11.70        19.56         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.82        24.76        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         3.72         5.39        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        0.49        15.81        16.44         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98        14.17         0.53        12.82         0.66        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         3.42        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         8.05        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85        13.35        17.19        15.98        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.25        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53        60.56        20.15        37.64         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        48.79        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       11.70        11.93        61.22        18.74        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        52.24         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
        6.58         5.72        21.04         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       18.41        40.08        28.41        32.94        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        10.62         0.79 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        0.1                         0.0 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                      68.02                      122.30 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                      11.90                       12.79 
[1] "0.1 - 68.0 (11.9)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.5"
D11V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(6Q21) MUTATED         3        1       10        5         7
  AMP PEAK 11(6Q21) WILD-TYPE       8       18       38       27        70
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(6Q21) MUTATED          13         5         22         12
  AMP PEAK 11(6Q21) WILD-TYPE        71        24         75         60
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(6Q21) MUTATED            6       16         2
  AMP PEAK 11(6Q21) WILD-TYPE         42       35         2
D11V3, multiclass
            clus
vv           AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  STAGE I                            3                           8
  STAGE IA                           1                          18
  STAGE IB                          10                          38
  STAGE II                           5                          27
  STAGE IIA                          7                          70
  STAGE IIB                         13                          71
  STAGE III                          5                          24
  STAGE IIIA                        22                          75
  STAGE IIIB                        12                          60
  STAGE IIIC                         6                          42
  STAGE IV                          16                          35
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 11(6Q21) MUTATED       7  24  46  26
  AMP PEAK 11(6Q21) WILD-TYPE    46 102 234  98
D11V4, multiclass
       clus
vv      AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1                         7                          46
  T2                           24                         102
  T3                           46                         234
  T4                           26                          98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 11(6Q21) MUTATED    29  35  19  19
  AMP PEAK 11(6Q21) WILD-TYPE 171 147  77  78
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        29                         171
  N1                        35                         147
  N2                        19                          77
  N3                        19                          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"
D11V6, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    87  13
  AMP PEAK 11(6Q21) WILD-TYPE 426  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     87   13
  AMP PEAK 11(6Q21) WILD-TYPE  426   26
   clus
vv  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  0                        87                         426
  1                        13                          26
[1] 2 2
[1] FALSE
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    29  79
  AMP PEAK 11(6Q21) WILD-TYPE 153 348
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     29   79
  AMP PEAK 11(6Q21) WILD-TYPE  153  348
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                        29                         153
  MALE                          79                         348
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 11(6Q21) MUTATED                                       7
  AMP PEAK 11(6Q21) WILD-TYPE                                    64
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(6Q21) MUTATED                                                       28
  AMP PEAK 11(6Q21) WILD-TYPE                                                    134
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(6Q21) MUTATED                                                                  22
  AMP PEAK 11(6Q21) WILD-TYPE                                                                59
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 11(6Q21) MUTATED                                                 19
  AMP PEAK 11(6Q21) WILD-TYPE                                               59
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 11(6Q21) MUTATED                                                          1
  AMP PEAK 11(6Q21) WILD-TYPE                                                       20
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 11(6Q21) MUTATED                                                           2
  AMP PEAK 11(6Q21) WILD-TYPE                                                         6
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 11(6Q21) MUTATED                                          2
  AMP PEAK 11(6Q21) WILD-TYPE                                       11
D11V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 11(6Q21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  AMP PEAK 11(6Q21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     2 106
  AMP PEAK 11(6Q21) WILD-TYPE   4 497
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      2  106
  AMP PEAK 11(6Q21) WILD-TYPE    4  497
     clus
vv    AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  NO                          2                           4
  YES                       106                         497
[1] 2 2
[1] FALSE
D11V10, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 11(6Q21) MUTATED    61   2   6   6
  AMP PEAK 11(6Q21) WILD-TYPE 286  16  13  19
D11V11, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  R0                        61                         286
  R1                         2                          16
  R2                         6                          13
  RX                         6                          19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(6Q21) MUTATED      18                         4
  AMP PEAK 11(6Q21) WILD-TYPE   111                         9
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(6Q21) MUTATED                                           1    69
  AMP PEAK 11(6Q21) WILD-TYPE                                         0   316
D11V13, multiclass
                                           clus
vv                                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                                            18
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            69
                                           clus
vv                                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                                             111
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     1  62
  AMP PEAK 11(6Q21) WILD-TYPE   6 332
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      1   62
  AMP PEAK 11(6Q21) WILD-TYPE    6  332
                        clus
vv                       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                        62                         332
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(7P22.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(7P22.3) MUTATED   196 129
  AMP PEAK 12(7P22.3) WILD-TYPE 158  92
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          325                           250 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          129                            92 
$`AMP PEAK 12(7P22.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC 
       32.45         7.69        33.27        20.09         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 
       18.64         0.53        17.03         0.79        23.41         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       42.77        21.70        23.18        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       32.61        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90        29.00         7.13         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        0.36         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       12.92        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10        12.59        12.49        12.76        12.59         0.10 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03         0.13         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC 
       14.70         7.04        29.59        53.95         9.30         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       12.69         7.00        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        9.27         4.44        18.81        22.82         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        28.11        18.18        42.87        46.19        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 
       15.91        10.16         2.10         2.66        19.73        11.70 
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 
       11.01         6.61         6.97         4.64        18.35        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
       19.33         9.17        32.78        25.61        18.05        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        18.15 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
        3.45        12.76        18.71        14.43        11.44         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8370 
        6.18        19.50        13.08        22.19         0.95         3.32 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       14.79         0.26         5.39         9.21        20.22         1.12 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       16.44         9.86         8.22        10.68        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 
       22.26         1.48        12.89         0.72         0.53        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       13.51        20.42         1.15        13.64         3.25        13.18 
TCGA-CD-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         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
       11.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       14.01        19.07        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 
       22.98        36.00        12.03        28.96         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.66        11.93        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-F1-6874 TCGA-F1-6875 
       14.27        16.44        15.16         2.96        14.47        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 
        3.48        19.53        14.07        22.29        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 
        5.52         0.23        26.47        12.59        14.17        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.25        10.19         2.10        12.95        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        9.67        27.42         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 
        5.19         1.41         6.44         6.51         1.81         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 
        8.52        61.25         6.08         8.61       122.30        57.44 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       35.24        21.73        34.45         7.73        34.29        46.26 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY 
        2.50        12.79         2.70        17.85        27.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        36.69        11.70        11.93        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D 
        1.71         7.36         9.50         2.01         4.54        64.18 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        29.98        54.12        16.14        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK 12(7P22.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3YA 
       31.27        14.30        58.55         4.21         6.21        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        2.63         3.88         9.30        12.82         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       12.16        41.52        25.41        31.56        24.03         6.28 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
       19.99        21.01         7.17         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L 
        7.40        13.48         7.76        21.37        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.66         0.10        12.46        22.39        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6XQ 
        4.47        12.23        13.18        33.11         5.16         6.35 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8ER 
       15.78         2.89        20.02         4.80        19.96        12.43 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-A5TI 
       30.71        15.06         9.17         3.42        26.70        19.56 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        9.47         9.44         7.43        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       26.10        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       32.94        12.82        23.93        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        9.07        17.49         0.69        12.26         9.60        20.55 
TCGA-BR-8291 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       16.31         0.26        17.52        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 
       11.80        19.17        15.85         3.72        25.18        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       11.54        15.81        15.68        12.56         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       13.51         8.98        14.17        12.82         0.66         0.46 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       20.65        11.57         5.13         2.83        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.10         0.10         9.34         0.10        12.62         3.02 
TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        1.02        29.98        47.05        12.03         0.00         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5577 
      105.07        15.02        79.07        65.10        69.04        12.36 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 
       20.55        18.61        17.85        13.35        10.26        12.79 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.80        19.50         5.92        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.99        16.24 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB 
       21.27        11.38        59.54         5.03        13.58        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        14.27        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76        24.30         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.98         6.51         0.26        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       21.21         5.36        13.08         6.74        12.59         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 
        7.82        13.51         2.53         3.72        19.73         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      115.69       116.38        71.38        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PD 
        0.92        18.48        27.88        32.48        28.96        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       22.19         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91Y 
       26.24        64.57        61.22        22.68        36.16         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
       52.24         9.04        55.43         6.58         5.72         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J 
       28.41        17.13        26.04        21.11 

  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                       12.760                        12.725 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7P22.3) MUTATED         9        9       25       15        41
  AMP PEAK 12(7P22.3) WILD-TYPE       2       10       23       17        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7P22.3) MUTATED          49        23         53         34
  AMP PEAK 12(7P22.3) WILD-TYPE        35         6         44         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(7P22.3) MUTATED           29       26         3
  AMP PEAK 12(7P22.3) WILD-TYPE         19       25         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  STAGE I                              9                             2
  STAGE IA                             9                            10
  STAGE IB                            25                            23
  STAGE II                            15                            17
  STAGE IIA                           41                            36
  STAGE IIB                           49                            35
  STAGE III                           23                             6
  STAGE IIIA                          53                            44
  STAGE IIIB                          34                            38
  STAGE IIIC                          29                            19
  STAGE IV                            26                            25
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 12(7P22.3) MUTATED      34  64 165  59
  AMP PEAK 12(7P22.3) WILD-TYPE    19  62 115  65
D12V4, multiclass
       clus
vv      AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  T0+T1                          34                            19
  T2                             64                            62
  T3                            165                           115
  T4                             59                            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 12(7P22.3) MUTATED   108 104  56  52
  AMP PEAK 12(7P22.3) WILD-TYPE  92  78  40  45
D12V5, multiclass
    clus
vv   AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  N0                         108                            92
  N1                         104                            78
  N2                          56                            40
  N3                          52                            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"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED   280  21
  AMP PEAK 12(7P22.3) WILD-TYPE 233  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED    280   21
  AMP PEAK 12(7P22.3) WILD-TYPE  233   18
   clus
vv  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  0                         280                           233
  1                          21                            18
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED    83 261
  AMP PEAK 12(7P22.3) WILD-TYPE  99 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED     83  261
  AMP PEAK 12(7P22.3) WILD-TYPE   99  166
        clus
vv       AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  FEMALE                          83                            99
  MALE                           261                           166
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 12(7P22.3) MUTATED                                      24
  AMP PEAK 12(7P22.3) WILD-TYPE                                    47
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7P22.3) MUTATED                                                       80
  AMP PEAK 12(7P22.3) WILD-TYPE                                                     82
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(7P22.3) MUTATED                                                                  51
  AMP PEAK 12(7P22.3) WILD-TYPE                                                                30
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 12(7P22.3) MUTATED                                                 44
  AMP PEAK 12(7P22.3) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 12(7P22.3) MUTATED                                                          9
  AMP PEAK 12(7P22.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 12(7P22.3) MUTATED                                                           5
  AMP PEAK 12(7P22.3) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 12(7P22.3) MUTATED                                          9
  AMP PEAK 12(7P22.3) WILD-TYPE                                        4
D12V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 12(7P22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     80
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
                                                                   clus
vv                                                                  AMP PEAK 12(7P22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       82
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED     3 341
  AMP PEAK 12(7P22.3) WILD-TYPE   3 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED      3  341
  AMP PEAK 12(7P22.3) WILD-TYPE    3  262
     clus
vv    AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  NO                            3                             3
  YES                         341                           262
[1] 2 2
[1] FALSE
D12V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(7P22.3) MUTATED   181   8   9  12
  AMP PEAK 12(7P22.3) WILD-TYPE 166  10  10  13
D12V11, multiclass
    clus
vv   AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  R0                         181                           166
  R1                           8                            10
  R2                           9                            10
  RX                          12                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(7P22.3) MUTATED      73                         9
  AMP PEAK 12(7P22.3) WILD-TYPE    56                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(7P22.3) MUTATED                                           1   216
  AMP PEAK 12(7P22.3) WILD-TYPE                                         0   169
D12V13, multiclass
                                           clus
vv                                          AMP PEAK 12(7P22.3) MUTATED
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             216
                                           clus
vv                                          AMP PEAK 12(7P22.3) WILD-TYPE
  ASIAN                                                                56
  BLACK OR AFRICAN AMERICAN                                             4
  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"
D12V14, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED     6 206
  AMP PEAK 12(7P22.3) WILD-TYPE   1 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED      6  206
  AMP PEAK 12(7P22.3) WILD-TYPE    1  188
                        clus
vv                       AMP PEAK 12(7P22.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         206
                        clus
vv                       AMP PEAK 12(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           188
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7P11.2) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7P11.2) MUTATED   185 127
  AMP PEAK 13(7P11.2) WILD-TYPE 169  94
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          312                           263 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          127                            94 
$`AMP PEAK 13(7P11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69        20.09         0.85        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        0.53        17.03         0.79        23.41        14.50        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       60.39        68.02        21.70        23.18        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       32.61        21.01        47.93        18.35         3.32         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        8.71         2.60         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       10.36         5.92        13.41         0.10        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.59         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       25.25        12.00        12.03         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
        8.02         7.59         5.06        14.70         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81        19.96         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        18.18        42.87        46.19        15.91        10.16 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
        2.66        19.73        11.70        11.01         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 
        4.64        18.35        17.29        19.33         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       25.61        18.05        21.11         9.21        24.76        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.42        18.15         3.45        12.76        18.71        14.43 
TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.69         8.05         0.56         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 
       13.08        17.52         0.95         3.32        14.79         0.26 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        5.39        20.22         1.12        16.44         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68        13.87        22.26         1.48        12.89         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.17         0.53        19.36        13.51        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 
        3.25        13.18         0.07         0.10         0.16         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10         3.42        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4460 
       20.02        27.02        15.95         7.99         4.01        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 
       18.97         7.07        12.00        22.98        36.00        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       28.96        79.07        21.07         7.99        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       19.13        18.84        18.54        17.19        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       11.31        12.33        24.72        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 
       21.14        20.91        16.44        15.16        11.31         2.96 
TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       15.65        14.47        72.23         3.48        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 
       17.06         0.56         5.52         0.23        26.47         5.92 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       14.17        24.30        12.30         3.25        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.25        10.19         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       19.36        23.84        27.42         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.19         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        6.51         1.81         5.56        60.56        20.15        37.64 
TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT 
        9.86        18.21         8.52        61.25         6.08         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT 
       16.67       122.30       115.69        57.44         8.94        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.45        34.29         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
        1.87        27.35        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        18.74        20.81         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O 
        9.50        52.24         9.04         2.01         4.54        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        22.09        40.08        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        16.14        21.11        12.43        10.62         0.79 

$`AMP PEAK 13(7P11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        14.30        58.55         4.21         6.21        33.27 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         3.88         9.30        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         4.67        12.16       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43M 
       42.77        25.41        31.56        24.03         6.28         8.94 
TCGA-L5-A4OI TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI 
       19.99         7.17         7.43        25.12         7.40        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
        7.76        21.37        83.24        10.45        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       13.15        22.39        11.54         4.47        10.52        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-VR-A8EQ 
       13.18        33.11        29.59        15.78         4.80        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       12.43        18.31        15.06        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 
        2.10        26.70        19.56         9.47         9.44         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-6707 TCGA-BR-6709 
       13.87        13.68        39.12        26.10        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 
        8.98        30.90        31.20        32.94        12.82        23.93 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 
       28.01        15.32        28.73        12.43         9.07        17.49 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 
       11.44        12.26         9.60        20.55        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 
       16.31         6.18        19.50         0.26        22.19        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 
        4.31        14.04        11.80        19.17        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
        6.28         7.53         0.49        11.54        15.81        15.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56         7.53         6.08        13.41        13.51         8.98 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL 
       12.82         0.66         0.46        20.65         1.15        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-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 
        0.07         0.07         0.13         0.10         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 
       11.31        12.43         0.10        12.62         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 
        4.01        69.04        12.36        20.55        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 
       13.35        10.26        12.79        10.55        16.80        19.50 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27         5.92        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7998 
        0.62         7.99        16.24        21.27        11.38        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
       59.54         5.03        13.58        18.08         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       12.59        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
       11.84        24.20        22.75        21.37        29.98         6.51 
TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        5.36        13.08         5.56         7.82        13.51         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        3.72        19.73        45.67         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
        5.13        37.91        40.64       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87        19.04         5.79         0.92        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO 
        7.73        28.96        46.26        16.31        22.19         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K 
       23.41        15.65        13.35        26.24        64.57        61.22 
TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       22.68         9.73        55.43         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        18.41        28.41        17.13        26.04 

  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                        122.3                         122.1 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                       12.905                        12.590 
[1] "0.1 - 122.3 (12.9)" "0.0 - 122.1 (12.6)"
[1] "hr=" "1.2"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(7P11.2) MUTATED         9       10       25       13        38
  AMP PEAK 13(7P11.2) WILD-TYPE       2        9       23       19        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(7P11.2) MUTATED          47        21         52         36
  AMP PEAK 13(7P11.2) WILD-TYPE        37         8         45         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(7P11.2) MUTATED           27       22         3
  AMP PEAK 13(7P11.2) WILD-TYPE         21       29         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  STAGE I                              9                             2
  STAGE IA                            10                             9
  STAGE IB                            25                            23
  STAGE II                            13                            19
  STAGE IIA                           38                            39
  STAGE IIB                           47                            37
  STAGE III                           21                             8
  STAGE IIIA                          52                            45
  STAGE IIIB                          36                            36
  STAGE IIIC                          27                            21
  STAGE IV                            22                            29
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 13(7P11.2) MUTATED      34  56 160  58
  AMP PEAK 13(7P11.2) WILD-TYPE    19  70 120  66
D13V4, multiclass
       clus
vv      AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  T0+T1                          34                            19
  T2                             56                            70
  T3                            160                           120
  T4                             58                            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
  AMP PEAK 13(7P11.2) MUTATED   107  98  52  49
  AMP PEAK 13(7P11.2) WILD-TYPE  93  84  44  48
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  N0                         107                            93
  N1                          98                            84
  N2                          52                            44
  N3                          49                            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"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED   271  16
  AMP PEAK 13(7P11.2) WILD-TYPE 242  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED    271   16
  AMP PEAK 13(7P11.2) WILD-TYPE  242   23
   clus
vv  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  0                         271                           242
  1                          16                            23
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED    82 248
  AMP PEAK 13(7P11.2) WILD-TYPE 100 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED     82  248
  AMP PEAK 13(7P11.2) WILD-TYPE  100  179
        clus
vv       AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  FEMALE                          82                           100
  MALE                           248                           179
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 13(7P11.2) MUTATED                                      25
  AMP PEAK 13(7P11.2) WILD-TYPE                                    46
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7P11.2) MUTATED                                                       76
  AMP PEAK 13(7P11.2) WILD-TYPE                                                     86
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(7P11.2) MUTATED                                                                  48
  AMP PEAK 13(7P11.2) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 13(7P11.2) MUTATED                                                 43
  AMP PEAK 13(7P11.2) WILD-TYPE                                               35
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 13(7P11.2) MUTATED                                                          7
  AMP PEAK 13(7P11.2) WILD-TYPE                                                       14
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 13(7P11.2) MUTATED                                                           3
  AMP PEAK 13(7P11.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 13(7P11.2) MUTATED                                          9
  AMP PEAK 13(7P11.2) WILD-TYPE                                        4
D13V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 13(7P11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     76
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           43
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
                                                                   clus
vv                                                                  AMP PEAK 13(7P11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        46
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       86
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED     2 328
  AMP PEAK 13(7P11.2) WILD-TYPE   4 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED      2  328
  AMP PEAK 13(7P11.2) WILD-TYPE    4  275
     clus
vv    AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  NO                            2                             4
  YES                         328                           275
[1] 2 2
[1] FALSE
D13V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(7P11.2) MUTATED   174   9   8  11
  AMP PEAK 13(7P11.2) WILD-TYPE 173   9  11  14
D13V11, multiclass
    clus
vv   AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  R0                         174                           173
  R1                           9                             9
  R2                           8                            11
  RX                          11                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(7P11.2) MUTATED      70                        11
  AMP PEAK 13(7P11.2) WILD-TYPE    59                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(7P11.2) MUTATED                                           1   206
  AMP PEAK 13(7P11.2) WILD-TYPE                                         0   179
D13V13, multiclass
                                           clus
vv                                          AMP PEAK 13(7P11.2) MUTATED
  ASIAN                                                              70
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             206
                                           clus
vv                                          AMP PEAK 13(7P11.2) WILD-TYPE
  ASIAN                                                                59
  BLACK OR AFRICAN AMERICAN                                             2
  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"
D13V14, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED     4 199
  AMP PEAK 13(7P11.2) WILD-TYPE   3 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED      4  199
  AMP PEAK 13(7P11.2) WILD-TYPE    3  195
                        clus
vv                       AMP PEAK 13(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         199
                        clus
vv                       AMP PEAK 13(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           195
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7Q21.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(7Q21.2) MUTATED   176 115
  AMP PEAK 14(7Q21.2) WILD-TYPE 178 106
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          291                           284 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          115                           106 
$`AMP PEAK 14(7Q21.2) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
       31.27         8.94        16.24        32.45         7.69        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63        20.12         0.53        17.03        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
       14.50        44.75        60.39        68.02         3.68        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E 
       21.70        23.18        31.56        25.22         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        24.00         4.70        32.61        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.13         6.94         2.60         0.36         3.95         3.02 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.45        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 
        0.10        15.52        11.54        12.33        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        12.03         0.13         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.04        29.59         6.35         9.30         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       18.81        19.96         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       10.16         2.10        19.73        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 
        9.44         6.97         4.64        18.35        17.29        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
       26.10         9.17        32.78        25.61        18.05        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 
       14.43        11.44         8.05         0.56         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
        7.40        13.08        17.52         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 
        0.26         5.39        25.18        20.22         1.12        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J2 
        9.86        10.68        13.87        12.89         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 
        0.53        13.51        20.65        20.42         1.15         3.25 
TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 
       13.18         0.07         0.10         0.13         0.16         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         3.42        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.20        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 
       54.08         4.01        14.01        12.03        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
       12.00        22.98        36.00        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       79.07        21.07        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.79        24.72        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 
       20.91        16.44        15.16        11.24        11.31         2.96 
TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       15.65        14.47        72.23         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 
       17.06         0.56         0.23        26.47         5.92        14.17 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       24.30        12.30        25.81         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-8663 
       10.19         2.10        12.95        19.36         3.45         3.39 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19         1.41         6.44         6.51         5.56         1.81 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        5.56        60.56        20.15         9.86         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        6.08         8.61       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        8.94        48.79        13.25        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.45         7.73        34.29         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       17.85         1.87        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        20.81        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         2.01         4.54        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       11.24        18.41        32.94        29.98        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

$`AMP PEAK 14(7Q21.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
        4.21         6.21        33.27         0.85        20.78        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        3.88         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC 
       12.16       122.10        41.52        25.41        24.03         6.28 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OP 
        4.31         8.94         3.68        19.99        21.01         7.17 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NI 
        7.43         8.71        25.12         7.40        55.50        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-LN-A49M 
        7.76         5.49        21.37         8.71        83.24        12.66 
TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.43        13.25        22.39        13.22         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.23        13.18        33.11         5.16         5.06        14.70 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-V5-A7RE TCGA-V5-AASX 
       53.95        15.78         1.45        20.02         4.80         4.44 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       22.82        12.43        42.87        15.91         3.42         2.66 
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
       26.70         9.47         6.61         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       39.12        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       32.94        12.82        23.93        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8077 
       28.73        12.43         3.45         9.07        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26         9.60        20.55        12.95         2.66        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 
        6.18        19.50         0.26        22.19        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 
       14.04        11.80        19.17        15.85         3.72         9.21 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        15.81        15.68         8.22        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI 
        8.98        12.82         0.66        19.36         0.46        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 
        0.07         0.07         0.07         0.10         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
       11.31         0.10        12.62         1.02         8.05        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 
       47.05        19.07        21.99         0.00         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 
       65.10         4.01        69.04         7.99        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.61        17.85        10.55        11.31        12.33        16.80 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       18.21        14.27         5.92        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        0.62         7.99        16.24        21.27        11.38        14.07 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03        13.58         5.52        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       14.27        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        11.84        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.37        29.98         6.51         0.26        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V 
       18.38         5.36        13.08         6.74        12.59         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       13.51         2.53        37.64         3.72        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       18.21         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92         5.46        13.02        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        46.26        16.31        22.19         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K 
       15.65        13.35        26.24        27.35        64.57        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
       18.74         9.73        52.24         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        5.72         2.66        22.09        40.08        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                        122.3                         122.1 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                        12.89                         12.59 
[1] "0.1 - 122.3 (12.9)" "0.0 - 122.1 (12.6)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(7Q21.2) MUTATED         7        8       24       16        42
  AMP PEAK 14(7Q21.2) WILD-TYPE       4       11       24       16        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(7Q21.2) MUTATED          40        15         45         37
  AMP PEAK 14(7Q21.2) WILD-TYPE        44        14         52         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(7Q21.2) MUTATED           26       22         3
  AMP PEAK 14(7Q21.2) WILD-TYPE         22       29         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  STAGE I                              7                             4
  STAGE IA                             8                            11
  STAGE IB                            24                            24
  STAGE II                            16                            16
  STAGE IIA                           42                            35
  STAGE IIB                           40                            44
  STAGE III                           15                            14
  STAGE IIIA                          45                            52
  STAGE IIIB                          37                            35
  STAGE IIIC                          26                            22
  STAGE IV                            22                            29
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 14(7Q21.2) MUTATED      30  62 149  50
  AMP PEAK 14(7Q21.2) WILD-TYPE    23  64 131  74
D14V4, multiclass
       clus
vv      AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  T0+T1                          30                            23
  T2                             62                            64
  T3                            149                           131
  T4                             50                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(7Q21.2) MUTATED   104  82  53  49
  AMP PEAK 14(7Q21.2) WILD-TYPE  96 100  43  48
D14V5, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  N0                         104                            96
  N1                          82                           100
  N2                          53                            43
  N3                          49                            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"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED   254  18
  AMP PEAK 14(7Q21.2) WILD-TYPE 259  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED    254   18
  AMP PEAK 14(7Q21.2) WILD-TYPE  259   21
   clus
vv  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  0                         254                           259
  1                          18                            21
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED    75 234
  AMP PEAK 14(7Q21.2) WILD-TYPE 107 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED     75  234
  AMP PEAK 14(7Q21.2) WILD-TYPE  107  193
        clus
vv       AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  FEMALE                          75                           107
  MALE                           234                           193
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 14(7Q21.2) MUTATED                                      26
  AMP PEAK 14(7Q21.2) WILD-TYPE                                    45
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(7Q21.2) MUTATED                                                       75
  AMP PEAK 14(7Q21.2) WILD-TYPE                                                     87
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(7Q21.2) MUTATED                                                                  50
  AMP PEAK 14(7Q21.2) WILD-TYPE                                                                31
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 14(7Q21.2) MUTATED                                                 33
  AMP PEAK 14(7Q21.2) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 14(7Q21.2) MUTATED                                                          8
  AMP PEAK 14(7Q21.2) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 14(7Q21.2) MUTATED                                                           4
  AMP PEAK 14(7Q21.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 14(7Q21.2) MUTATED                                          5
  AMP PEAK 14(7Q21.2) WILD-TYPE                                        8
D14V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 14(7Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     75
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 14(7Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       87
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED     2 307
  AMP PEAK 14(7Q21.2) WILD-TYPE   4 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED      2  307
  AMP PEAK 14(7Q21.2) WILD-TYPE    4  296
     clus
vv    AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  NO                            2                             4
  YES                         307                           296
[1] 2 2
[1] FALSE
D14V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(7Q21.2) MUTATED   168   5   7  11
  AMP PEAK 14(7Q21.2) WILD-TYPE 179  13  12  14
D14V11, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  R0                         168                           179
  R1                           5                            13
  R2                           7                            12
  RX                          11                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(7Q21.2) MUTATED      66                        11
  AMP PEAK 14(7Q21.2) WILD-TYPE    63                         2
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(7Q21.2) MUTATED                                           1   192
  AMP PEAK 14(7Q21.2) WILD-TYPE                                         0   193
D14V13, multiclass
                                           clus
vv                                          AMP PEAK 14(7Q21.2) MUTATED
  ASIAN                                                              66
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             192
                                           clus
vv                                          AMP PEAK 14(7Q21.2) WILD-TYPE
  ASIAN                                                                63
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED     5 187
  AMP PEAK 14(7Q21.2) WILD-TYPE   2 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED      5  187
  AMP PEAK 14(7Q21.2) WILD-TYPE    2  207
                        clus
vv                       AMP PEAK 14(7Q21.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         187
                        clus
vv                       AMP PEAK 14(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           207
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8P23.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(8P23.1) MUTATED   129  79
  AMP PEAK 15(8P23.1) WILD-TYPE 225 142
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          208                           367 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                           79                           142 
$`AMP PEAK 15(8P23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        14.30         8.94        16.24        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A939 
       20.09        20.78         4.67       122.10        68.02        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT 
       19.99        21.01        47.93        18.35         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.13         0.36        55.50        12.92        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49U 
        5.49        21.37         8.71        10.36         5.92        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A7HZ TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 
        0.10         0.10        13.18         7.59         5.06        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
       12.69         7.00         4.80        15.35        19.96        22.82 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       10.16        19.73        26.70        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.97         4.64        30.90        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 
       13.68        19.33        25.61        19.89        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-8060 
       32.94        35.24        23.93        18.15         9.07        11.44 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 
       12.26         8.05         2.66         7.40         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 
        3.32        19.17         0.26        15.85         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.22         9.34        13.45         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       13.41        14.17        12.82        19.36         0.46        20.42 
TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8536 
       11.57         3.25         0.07         0.07         0.16         0.10 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4441 
        9.34        11.61         6.58        12.62        15.95        14.01 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         0.00        18.97         7.07        12.00 
TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 
        0.99        28.96        65.10        21.07        12.66        11.93 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        10.26        12.79        10.55        11.31        12.33 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       18.21        14.66        20.91         5.92        15.16        14.76 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.31        11.44         2.96         8.38         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         5.52        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        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93G 
        8.81         5.19        12.59         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR 
       37.64        19.73         9.86        45.67        61.25         6.08 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT 
       16.67       115.69        35.61        16.87        19.04        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
        5.46        27.88        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        2.70         9.27        23.41        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V 
       14.33        11.93        61.22        18.74        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U 
        7.36         4.54         5.72        21.04        42.54        22.09 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

$`AMP PEAK 15(8P23.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       31.27        58.55         7.63         5.92        13.94         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69         6.21         0.85         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86        14.50        12.16        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       60.39         3.68        41.52        42.77        25.41        23.18 
TCGA-KH-A6WC TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        6.28         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       32.61         3.32         7.17         1.38        58.59        29.00 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45        20.02        20.38         5.29         3.42 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        9.27         4.44        18.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 
        2.66        11.70        19.56         9.44         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 
        6.18         9.57         6.61        17.29        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        18.05        12.16         8.98        21.11 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       12.82         9.21        24.76        15.42        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         3.45        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       14.43         0.69         9.60        20.55         0.56        12.95 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20        15.58         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 
        0.26        22.19        17.52         0.95        26.33        11.80 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       14.79         3.72         9.21         1.12        12.79        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 
        6.08        13.51        12.89         8.98         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.66        13.51        20.65         1.15        13.64         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 
        2.83        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         3.42        11.31        12.43        12.20         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 
       54.08         4.01        29.98        47.05        19.07         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
        6.02       105.07        12.03        15.02        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       69.04         7.99        12.36        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        13.35        17.19        15.22        15.98 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19        21.14        14.27 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       16.44        13.78        13.71         9.76        15.65         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56         0.23         1.51         5.92        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD 
       14.17        12.10        10.62         0.76         5.59        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H6 
       11.77        21.37         6.51         6.25        10.19         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
        5.36        13.08         1.41         6.44         6.74         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
        1.81         7.82        13.51         2.53         5.56         3.72 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       18.21         8.52         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94         5.79         0.92        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        32.48         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       46.26         2.50        12.79        17.85         1.87        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91S TCGA-VQ-A91U 
       13.35        65.16        36.69        11.70        22.68         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58        64.18         2.66        11.24        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6K 
       12.43 

  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                         0.00                          0.07 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                        122.1                         122.3 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                        13.94                         12.43 
[1] "0.0 - 122.1 (13.9)" "0.1 - 122.3 (12.4)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8P23.1) MUTATED         4        9       21       13        23
  AMP PEAK 15(8P23.1) WILD-TYPE       7       10       27       19        54
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8P23.1) MUTATED          36         8         34         20
  AMP PEAK 15(8P23.1) WILD-TYPE        48        21         63         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8P23.1) MUTATED           19       21         2
  AMP PEAK 15(8P23.1) WILD-TYPE         29       30         2
D15V3, multiclass
            clus
vv           AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  STAGE I                              4                             7
  STAGE IA                             9                            10
  STAGE IB                            21                            27
  STAGE II                            13                            19
  STAGE IIA                           23                            54
  STAGE IIB                           36                            48
  STAGE III                            8                            21
  STAGE IIIA                          34                            63
  STAGE IIIB                          20                            52
  STAGE IIIC                          19                            29
  STAGE IV                            21                            30
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 15(8P23.1) MUTATED      23  48  94  50
  AMP PEAK 15(8P23.1) WILD-TYPE    30  78 186  74
D15V4, multiclass
       clus
vv      AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  T0+T1                          23                            30
  T2                             48                            78
  T3                             94                           186
  T4                             50                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 15(8P23.1) MUTATED    73  67  32  39
  AMP PEAK 15(8P23.1) WILD-TYPE 127 115  64  58
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  N0                          73                           127
  N1                          67                           115
  N2                          32                            64
  N3                          39                            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"
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED   192  14
  AMP PEAK 15(8P23.1) WILD-TYPE 321  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED    192   14
  AMP PEAK 15(8P23.1) WILD-TYPE  321   25
   clus
vv  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  0                         192                           321
  1                          14                            25
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED    87 138
  AMP PEAK 15(8P23.1) WILD-TYPE  95 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED     87  138
  AMP PEAK 15(8P23.1) WILD-TYPE   95  289
        clus
vv       AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  FEMALE                          87                            95
  MALE                           138                           289
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 15(8P23.1) MUTATED                                      30
  AMP PEAK 15(8P23.1) WILD-TYPE                                    41
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8P23.1) MUTATED                                                       59
  AMP PEAK 15(8P23.1) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(8P23.1) MUTATED                                                                  33
  AMP PEAK 15(8P23.1) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 15(8P23.1) MUTATED                                                 32
  AMP PEAK 15(8P23.1) WILD-TYPE                                               46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 15(8P23.1) MUTATED                                                         10
  AMP PEAK 15(8P23.1) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 15(8P23.1) MUTATED                                                           5
  AMP PEAK 15(8P23.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 15(8P23.1) MUTATED                                          5
  AMP PEAK 15(8P23.1) WILD-TYPE                                        8
D15V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 15(8P23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 15(8P23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED     4 221
  AMP PEAK 15(8P23.1) WILD-TYPE   2 382
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED      4  221
  AMP PEAK 15(8P23.1) WILD-TYPE    2  382
     clus
vv    AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  NO                            4                             2
  YES                         221                           382
[1] 2 2
[1] FALSE
D15V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(8P23.1) MUTATED   137   8   6  14
  AMP PEAK 15(8P23.1) WILD-TYPE 210  10  13  11
D15V11, multiclass
    clus
vv   AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  R0                         137                           210
  R1                           8                            10
  R2                           6                            13
  RX                          14                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(8P23.1) MUTATED      41                         5
  AMP PEAK 15(8P23.1) WILD-TYPE    88                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 15(8P23.1) MUTATED                                           0   145
  AMP PEAK 15(8P23.1) WILD-TYPE                                         1   240
D15V13, multiclass
                                           clus
vv                                          AMP PEAK 15(8P23.1) MUTATED
  ASIAN                                                              41
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             145
                                           clus
vv                                          AMP PEAK 15(8P23.1) WILD-TYPE
  ASIAN                                                                88
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED     4 141
  AMP PEAK 15(8P23.1) WILD-TYPE   3 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED      4  141
  AMP PEAK 15(8P23.1) WILD-TYPE    3  253
                        clus
vv                       AMP PEAK 15(8P23.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         141
                        clus
vv                       AMP PEAK 15(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8P11.21) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(8P11.21) MUTATED   155  92
  AMP PEAK 16(8P11.21) WILD-TYPE 199 129
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           247                            328 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                            92                            129 
$`AMP PEAK 16(8P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55        13.94         8.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D 
       33.27        20.09        20.78        18.64         3.88        17.03 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       12.82         4.67       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
        3.68        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        0.30         3.68        19.99        47.93        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A891 
        3.16         4.90         7.13         7.43         0.36         3.95 
TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       35.97        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
        8.71        13.41        27.12        10.36         5.92        10.45 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       13.15        15.35         0.10         0.10        12.46        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.59         0.10        11.54        12.33        12.03        13.18 
TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG 
        0.13         7.59         5.06        53.95        15.78        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP 
        7.00        20.02        20.38        15.35         4.44        19.96 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7I 
       22.82         8.12        28.11        18.18        46.19        15.91 
TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        2.10        26.70        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.97         4.64        30.90        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 
       17.29        13.68         9.17        19.89        12.16        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94         9.21        35.24        23.93        28.01 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 
        3.45         9.07        12.76        12.26         8.05        12.95 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
        7.40        19.50         4.31         3.32        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       15.85         5.39        20.22        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       13.45         7.53         8.22         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       13.41        12.82        19.36         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8530 TCGA-CD-8536 
       11.57         3.25         0.07         0.07         0.16         0.10 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        9.34        11.61         6.58        12.62        20.02        15.95 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4469 
        7.99        14.01        12.03        21.99         0.00         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
       12.00         6.97         0.99        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-6527 
       65.10        69.04        21.07        11.93        17.85        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV 
       12.79        10.55        12.33        14.66        20.91         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-A747 TCGA-D7-A748 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HF-A5NB 
        8.38         4.34        21.27        19.53         5.52        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 
       26.47        14.27        14.17        11.41        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       11.84        24.20         3.25        29.98         8.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        19.36        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        8.81        18.38         5.19         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        6.51         5.56         7.82         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73        45.67         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
        6.08       115.69        71.38        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       48.79        27.88        28.96        34.29        16.31         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91E TCGA-VQ-A91N 
        9.27        23.41        26.24        64.57        11.93        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 TCGA-VQ-A928 
       22.68         1.71        36.16         7.36         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZA-A8F6 
       64.18        21.04        22.09        40.08        32.94        10.62 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK 16(8P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        31.27         7.63         5.92        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L 
        6.21         0.85         2.63        20.12         9.30         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.79        23.41         9.96        14.86        14.50        12.16 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC 
       41.52        42.77        25.41        21.70        25.22         6.28 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T 
        7.17         1.38        58.59        29.00         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       12.92        13.48        16.47        83.24        52.57        46.09 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 
       12.66        12.43        13.41         0.10        13.25        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.49        22.39        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        10.52        12.00        12.23        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.89         1.45         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
        9.27        18.81        12.43         1.55        18.31        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD 
       42.87        15.06        11.24         9.17        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4191 
        2.66        19.73        11.70        19.56         7.43        18.35 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
        6.18         9.57         6.61        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 
       32.78        25.61        18.05         8.98        21.11        12.82 
TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        15.42        18.15        15.32        28.73        12.43 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       18.71        17.49        14.43        11.44         0.69         9.60 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.56         2.66        16.31         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 
       26.33        14.04        11.80        14.79         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.21         1.12         6.28         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         9.86        15.68        10.68        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QM 
        0.53         0.66        13.51        20.65         1.15         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 
        2.83        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         3.42        11.31        12.43        12.20         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         1.02         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 
       29.98        47.05        19.07         9.01        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97        36.00         1.02         0.99         6.02       105.07 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       79.07         4.01         7.99        12.36        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.22        15.98        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       17.19        18.21        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-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
        7.99        16.24        14.47        72.23        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        0.56         0.23         1.51         5.92        12.59        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       10.62         0.76         5.59        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 
       21.37         6.51         6.25        10.19        12.95         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       27.42        21.21         3.45        18.81         3.39         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A663 
       13.08         6.44         1.81        13.51         2.53         9.86 
TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N5 
       16.67       122.30        37.91        40.64       116.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        35.24        21.73        34.45        32.48         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        22.19         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        27.35        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       11.70        61.22        20.81         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94R 
        9.04         2.01        55.43         6.58         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       11.24        18.41        28.41        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        21.11        12.43 

  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                         122.1                          122.3 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                        12.760                         12.805 
[1] "0.0 - 122.1 (12.8)" "0.1 - 122.3 (12.8)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(8P11.21) MUTATED         6       11       23       15        27
  AMP PEAK 16(8P11.21) WILD-TYPE       5        8       25       17        50
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(8P11.21) MUTATED          45        16         37         22
  AMP PEAK 16(8P11.21) WILD-TYPE        39        13         60         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(8P11.21) MUTATED           24       19         3
  AMP PEAK 16(8P11.21) WILD-TYPE         24       32         1
D16V3, multiclass
            clus
vv           AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                             11                              8
  STAGE IB                             23                             25
  STAGE II                             15                             17
  STAGE IIA                            27                             50
  STAGE IIB                            45                             39
  STAGE III                            16                             13
  STAGE IIIA                           37                             60
  STAGE IIIB                           22                             50
  STAGE IIIC                           24                             24
  STAGE IV                             19                             32
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 16(8P11.21) MUTATED      28  56 114  55
  AMP PEAK 16(8P11.21) WILD-TYPE    25  70 166  69
D16V4, multiclass
       clus
vv      AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  T0+T1                           28                             25
  T2                              56                             70
  T3                             114                            166
  T4                              55                             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 16(8P11.21) MUTATED    88  89  33  39
  AMP PEAK 16(8P11.21) WILD-TYPE 112  93  63  58
D16V5, multiclass
    clus
vv   AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  N0                           88                            112
  N1                           89                             93
  N2                           33                             63
  N3                           39                             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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED   230  15
  AMP PEAK 16(8P11.21) WILD-TYPE 283  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED    230   15
  AMP PEAK 16(8P11.21) WILD-TYPE  283   24
   clus
vv  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  0                          230                            283
  1                           15                             24
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    90 176
  AMP PEAK 16(8P11.21) WILD-TYPE  92 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     90  176
  AMP PEAK 16(8P11.21) WILD-TYPE   92  251
        clus
vv       AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           90                             92
  MALE                            176                            251
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 16(8P11.21) MUTATED                                      29
  AMP PEAK 16(8P11.21) WILD-TYPE                                    42
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(8P11.21) MUTATED                                                       74
  AMP PEAK 16(8P11.21) WILD-TYPE                                                     88
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(8P11.21) MUTATED                                                                  31
  AMP PEAK 16(8P11.21) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 16(8P11.21) MUTATED                                                 29
  AMP PEAK 16(8P11.21) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 16(8P11.21) MUTATED                                                         11
  AMP PEAK 16(8P11.21) WILD-TYPE                                                       10
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 16(8P11.21) MUTATED                                                           5
  AMP PEAK 16(8P11.21) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 16(8P11.21) MUTATED                                          5
  AMP PEAK 16(8P11.21) WILD-TYPE                                        8
D16V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 16(8P11.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      74
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  AMP PEAK 16(8P11.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        88
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED     4 262
  AMP PEAK 16(8P11.21) WILD-TYPE   2 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED      4  262
  AMP PEAK 16(8P11.21) WILD-TYPE    2  341
     clus
vv    AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  NO                             4                              2
  YES                          262                            341
[1] 2 2
[1] FALSE
D16V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(8P11.21) MUTATED   142  10   6  15
  AMP PEAK 16(8P11.21) WILD-TYPE 205   8  13  10
D16V11, multiclass
    clus
vv   AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  R0                          142                            205
  R1                           10                              8
  R2                            6                             13
  RX                           15                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(8P11.21) MUTATED      58                         6
  AMP PEAK 16(8P11.21) WILD-TYPE    71                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 16(8P11.21) MUTATED                                           0
  AMP PEAK 16(8P11.21) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 16(8P11.21) MUTATED     163
  AMP PEAK 16(8P11.21) WILD-TYPE   222
D16V13, multiclass
                                           clus
vv                                          AMP PEAK 16(8P11.21) MUTATED
  ASIAN                                                               58
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              163
                                           clus
vv                                          AMP PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                                 71
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED     4 168
  AMP PEAK 16(8P11.21) WILD-TYPE   3 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED      4  168
  AMP PEAK 16(8P11.21) WILD-TYPE    3  226
                        clus
vv                       AMP PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          168
                        clus
vv                       AMP PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            226
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(8Q24.21) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(8Q24.21) MUTATED   253 163
  AMP PEAK 17(8Q24.21) WILD-TYPE 101  58
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           416                            159 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           163                             58 
$`AMP PEAK 17(8Q24.21) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         0.53        17.03         0.79        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        4.67        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         3.16        30.25         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         1.38         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG 
        7.43         2.60         0.36         3.95        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        27.12        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39         0.10        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        12.03        13.18         0.13         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        5.06        14.70         7.04        29.59        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       42.87        46.19        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.10        19.73        26.70        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         4.64        18.35        30.90         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 
       34.68        15.95        13.87        17.29        13.68         9.17 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       25.61        19.89        12.16        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       32.94         9.21        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73         3.45         9.07        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 
       14.43         0.69        12.26         9.60         8.05        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        2.66         2.20        15.58         7.40         6.18        13.08 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31        14.04         3.32        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       15.85         3.72         5.39         9.21        20.22        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 
        9.34        13.45         7.53        11.54        16.44         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        13.87         7.53        22.26         1.48        13.41 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
        0.72        14.17        12.82         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       11.57        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.10         0.16         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
        3.42         9.34        12.43        11.61         6.58        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00        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        36.00         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        69.04        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        14.66        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-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34         7.40         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       16.24        72.23        21.27         3.48        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52         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        23.84        12.30         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
        8.81        27.42         3.45         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51         5.56         1.81         7.82         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 
        9.24        11.05         8.61        16.67       115.69        71.38 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
       23.41        26.24        27.35        64.57        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       52.24         9.04         4.54         6.58         5.72        64.18 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`AMP PEAK 17(8Q24.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-JY-A6FH 
        6.21        18.64         9.30        23.41        14.86        42.77 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OP 
       25.22         6.28         8.94         3.68         4.70         7.17 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00         6.94         8.71        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A4A8 
        2.66        13.48        16.47        83.24        52.57        15.52 
TCGA-LN-A5U5 TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6XQ TCGA-R6-A6Y2 
        4.47        33.11         5.16         7.82         6.35         9.30 
TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA4G TCGA-X8-AAAR 
        1.45         3.42        18.81         1.55        15.06        10.16 
TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4280 
        2.66        11.70        19.56         6.61         7.43         6.61 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6710 
       19.33        39.12        26.10        32.78        18.05         8.98 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-8058 TCGA-BR-8060 
       12.82        24.76        15.32        12.43        17.49        11.44 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       20.55         0.56        16.31        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8487 
       17.52         0.95        11.80        14.79        25.18         1.12 
TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
       15.81         6.28         0.49        15.81         9.86        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
       12.56         6.08        13.51        12.89         8.98         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QM 
        0.66        19.36        13.51        20.65         1.15         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 
        2.83         3.25        13.18         0.07         0.13         0.10 
TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4304 TCGA-CG-4306 
        0.10        11.31        12.20         0.10        27.02         1.02 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        9.01        30.97         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 
       15.02        12.36        20.55        18.54        18.61        10.26 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY 
       16.80        19.50        17.19        18.21        21.14        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 
       13.71         9.76         7.13        14.47        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HU-8238 TCGA-HU-8604 
       22.29        59.54         5.03        13.58         1.51        12.10 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 
       10.62         5.59        21.37        10.19        12.95         9.67 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-AB1X TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       21.21        18.81        13.51         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8PC 
       40.64       116.38        57.44        21.73        32.48        46.26 
TCGA-VQ-A8PF TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
        2.50        15.65        13.35        14.33        65.16        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A94P 
       61.22        20.81         9.73         2.01        55.43         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6G 
       28.41        32.94        26.04 

  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                         122.1                          122.3 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                         12.66                          13.18 
[1] "0.0 - 122.1 (12.7)" "0.1 - 122.3 (13.2)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(8Q24.21) MUTATED         9       15       34       23        52
  AMP PEAK 17(8Q24.21) WILD-TYPE       2        4       14        9        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(8Q24.21) MUTATED          64        26         70         45
  AMP PEAK 17(8Q24.21) WILD-TYPE        20         3         27         27
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(8Q24.21) MUTATED           35       36         3
  AMP PEAK 17(8Q24.21) WILD-TYPE         13       15         1
D17V3, multiclass
            clus
vv           AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  STAGE I                               9                              2
  STAGE IA                             15                              4
  STAGE IB                             34                             14
  STAGE II                             23                              9
  STAGE IIA                            52                             25
  STAGE IIB                            64                             20
  STAGE III                            26                              3
  STAGE IIIA                           70                             27
  STAGE IIIB                           45                             27
  STAGE IIIC                           35                             13
  STAGE IV                             36                             15
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 17(8Q24.21) MUTATED      43  92 203  82
  AMP PEAK 17(8Q24.21) WILD-TYPE    10  34  77  42
D17V4, multiclass
       clus
vv      AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  T0+T1                           43                             10
  T2                              92                             34
  T3                             203                             77
  T4                              82                             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                              N0  N1  N2  N3
  AMP PEAK 17(8Q24.21) MUTATED   141 139  62  73
  AMP PEAK 17(8Q24.21) WILD-TYPE  59  43  34  24
D17V5, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  N0                          141                             59
  N1                          139                             43
  N2                           62                             34
  N3                           73                             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"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED   372  27
  AMP PEAK 17(8Q24.21) WILD-TYPE 141  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED    372   27
  AMP PEAK 17(8Q24.21) WILD-TYPE  141   12
   clus
vv  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  0                          372                            141
  1                           27                             12
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED   124 317
  AMP PEAK 17(8Q24.21) WILD-TYPE  58 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED    124  317
  AMP PEAK 17(8Q24.21) WILD-TYPE   58  110
        clus
vv       AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  FEMALE                          124                             58
  MALE                            317                            110
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 17(8Q24.21) MUTATED                                      41
  AMP PEAK 17(8Q24.21) WILD-TYPE                                    30
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(8Q24.21) MUTATED                                                      113
  AMP PEAK 17(8Q24.21) WILD-TYPE                                                     49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(8Q24.21) MUTATED                                                                  61
  AMP PEAK 17(8Q24.21) WILD-TYPE                                                                20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 17(8Q24.21) MUTATED                                                 57
  AMP PEAK 17(8Q24.21) WILD-TYPE                                               21
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 17(8Q24.21) MUTATED                                                         16
  AMP PEAK 17(8Q24.21) WILD-TYPE                                                        5
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 17(8Q24.21) MUTATED                                                           6
  AMP PEAK 17(8Q24.21) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 17(8Q24.21) MUTATED                                          9
  AMP PEAK 17(8Q24.21) WILD-TYPE                                        4
D17V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 17(8Q24.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
                                                                   clus
vv                                                                  AMP PEAK 17(8Q24.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         30
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED     5 436
  AMP PEAK 17(8Q24.21) WILD-TYPE   1 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED      5  436
  AMP PEAK 17(8Q24.21) WILD-TYPE    1  167
     clus
vv    AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  NO                             5                              1
  YES                          436                            167
[1] 2 2
[1] FALSE
D17V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(8Q24.21) MUTATED   239  15  12  20
  AMP PEAK 17(8Q24.21) WILD-TYPE 108   3   7   5
D17V11, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  R0                          239                            108
  R1                           15                              3
  R2                           12                              7
  RX                           20                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(8Q24.21) MUTATED      96                        12
  AMP PEAK 17(8Q24.21) WILD-TYPE    33                         1
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(8Q24.21) MUTATED                                           1
  AMP PEAK 17(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 17(8Q24.21) MUTATED     269
  AMP PEAK 17(8Q24.21) WILD-TYPE   116
D17V13, multiclass
                                           clus
vv                                          AMP PEAK 17(8Q24.21) MUTATED
  ASIAN                                                               96
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              269
                                           clus
vv                                          AMP PEAK 17(8Q24.21) WILD-TYPE
  ASIAN                                                                 33
  BLACK OR AFRICAN AMERICAN                                              1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED     5 280
  AMP PEAK 17(8Q24.21) WILD-TYPE   2 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED      5  280
  AMP PEAK 17(8Q24.21) WILD-TYPE    2  114
                        clus
vv                       AMP PEAK 17(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          280
                        clus
vv                       AMP PEAK 17(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            114
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(9P24.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(9P24.1) MUTATED    54  27
  AMP PEAK 18(9P24.1) WILD-TYPE 300 194
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           81                           494 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           27                           194 
$`AMP PEAK 18(9P24.1) MUTATED`
TCGA-2H-A9GL TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A939 
        5.92        17.03        12.82         9.96       122.10        21.70 
TCGA-L5-A43J TCGA-L5-A4OU TCGA-L5-A88Y TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NT 
        4.31        29.00         0.36        12.92         5.49        27.12 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V 
       10.36         5.92        12.43        13.41        13.15         0.10 
TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-Z6-AAPN 
       13.18         7.82        14.70        18.18         9.17         2.66 
TCGA-B7-A5TK TCGA-BR-4267 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7707 
        9.47         6.18        18.05        19.89        12.16        23.93 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 
       14.43         9.60         0.56         2.66         2.20        12.79 
TCGA-BR-8678 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5801 
       11.54        12.89         0.53        13.64         2.83        13.18 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4460 
        0.13        12.43        12.20         7.99         8.05        21.99 
TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EY 
       30.97        15.22        10.55        12.33        14.27        11.44 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB 
        0.62        16.24        72.23        21.27         0.23        18.08 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD 
       14.17        12.10        10.62         0.76        12.30        22.75 
TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-KB-A6F7 
        8.98         2.10        12.95        12.30         3.39        60.56 
TCGA-KB-A93G TCGA-R5-A7ZI TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S 
       20.15        61.25         5.46        46.26        23.41        22.68 
TCGA-VQ-A91V TCGA-VQ-A94T TCGA-VQ-AA6D 
       36.16        11.24        17.13 

$`AMP PEAK 18(9P24.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         3.88         9.30         0.53         0.79        23.41 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       68.02         3.68        41.52        42.77        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71         2.60        25.12         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.55        13.22         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R 
       83.24        52.57        46.09        10.45        12.66         0.10 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.23        12.03         0.13        33.11         5.16 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       53.95         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       42.87        46.19        15.06        11.24        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.44         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 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
        9.17        32.78        25.61         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        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        12.76        18.71        17.49        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 
        0.69        12.26        20.55         8.05        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.41        13.51         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.15        11.57         5.13         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        3.42         9.34        11.31        11.61         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 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 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.13         7.99        14.47        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56         5.52        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        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        7.82        13.51         2.53         5.56        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73         9.86        45.67        18.21         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92        48.79        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         1.87         9.27        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.93        61.22        18.74        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                        122.1                         122.3 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                        12.43                         12.79 
[1] "0.1 - 122.1 (12.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(9P24.1) MUTATED         2        3       10        3        13
  AMP PEAK 18(9P24.1) WILD-TYPE       9       16       38       29        64
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(9P24.1) MUTATED          11         3         12         11
  AMP PEAK 18(9P24.1) WILD-TYPE        73        26         85         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(9P24.1) MUTATED            9        6         0
  AMP PEAK 18(9P24.1) WILD-TYPE         39       45         4
D18V3, multiclass
            clus
vv           AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             3                            16
  STAGE IB                            10                            38
  STAGE II                             3                            29
  STAGE IIA                           13                            64
  STAGE IIB                           11                            73
  STAGE III                            3                            26
  STAGE IIIA                          12                            85
  STAGE IIIB                          11                            61
  STAGE IIIC                           9                            39
  STAGE IV                             6                            45
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 18(9P24.1) MUTATED      10  19  36  21
  AMP PEAK 18(9P24.1) WILD-TYPE    43 107 244 103
D18V4, multiclass
       clus
vv      AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  T0+T1                          10                            43
  T2                             19                           107
  T3                             36                           244
  T4                             21                           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 18(9P24.1) MUTATED    34  25   9  17
  AMP PEAK 18(9P24.1) WILD-TYPE 166 157  87  80
D18V5, multiclass
    clus
vv   AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  N0                          34                           166
  N1                          25                           157
  N2                           9                            87
  N3                          17                            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"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    76   5
  AMP PEAK 18(9P24.1) WILD-TYPE 437  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     76    5
  AMP PEAK 18(9P24.1) WILD-TYPE  437   34
   clus
vv  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  0                          76                           437
  1                           5                            34
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    23  65
  AMP PEAK 18(9P24.1) WILD-TYPE 159 362
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     23   65
  AMP PEAK 18(9P24.1) WILD-TYPE  159  362
        clus
vv       AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  FEMALE                          23                           159
  MALE                            65                           362
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 18(9P24.1) MUTATED                                       7
  AMP PEAK 18(9P24.1) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9P24.1) MUTATED                                                       24
  AMP PEAK 18(9P24.1) WILD-TYPE                                                    138
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(9P24.1) MUTATED                                                                   9
  AMP PEAK 18(9P24.1) WILD-TYPE                                                                72
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 18(9P24.1) MUTATED                                                 14
  AMP PEAK 18(9P24.1) WILD-TYPE                                               64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 18(9P24.1) MUTATED                                                          5
  AMP PEAK 18(9P24.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 18(9P24.1) MUTATED                                                           2
  AMP PEAK 18(9P24.1) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 18(9P24.1) MUTATED                                          3
  AMP PEAK 18(9P24.1) WILD-TYPE                                       10
D18V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 18(9P24.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 18(9P24.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             64
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED     3  85
  AMP PEAK 18(9P24.1) WILD-TYPE   3 518
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED      3   85
  AMP PEAK 18(9P24.1) WILD-TYPE    3  518
     clus
vv    AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  NO                            3                             3
  YES                          85                           518
[1] 2 2
[1] FALSE
D18V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(9P24.1) MUTATED    50   4   2   4
  AMP PEAK 18(9P24.1) WILD-TYPE 297  14  17  21
D18V11, multiclass
    clus
vv   AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  R0                          50                           297
  R1                           4                            14
  R2                           2                            17
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(9P24.1) MUTATED      24                         2
  AMP PEAK 18(9P24.1) WILD-TYPE   105                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(9P24.1) MUTATED                                           0    47
  AMP PEAK 18(9P24.1) WILD-TYPE                                         1   338
D18V13, multiclass
                                           clus
vv                                          AMP PEAK 18(9P24.1) MUTATED
  ASIAN                                                              24
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              47
                                           clus
vv                                          AMP PEAK 18(9P24.1) WILD-TYPE
  ASIAN                                                               105
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED     2  58
  AMP PEAK 18(9P24.1) WILD-TYPE   5 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED      2   58
  AMP PEAK 18(9P24.1) WILD-TYPE    5  336
                        clus
vv                       AMP PEAK 18(9P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       AMP PEAK 18(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           336
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(9P13.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 19(9P13.3) MUTATED    71  47
  AMP PEAK 19(9P13.3) WILD-TYPE 283 174
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          118                           457 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                           47                           174 
$`AMP PEAK 19(9P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD 
       25.78        14.30         5.92        12.82       122.10        68.02 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
        0.30         4.31        32.61        18.35         3.16        29.00 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
        0.36        55.50        35.97        27.12        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A4MQ TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FW 
        5.92        13.41        12.33        12.03        13.18         7.82 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EQ 
        5.06        14.70        15.78        20.38         9.27        22.82 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6707 
       18.18        42.87         9.17         9.47         6.61        19.89 
TCGA-BR-6709 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 
       12.16        23.93        18.15        18.71         9.60         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A44U 
       16.31         2.20        20.22        12.79        11.54        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5798 
        7.53        22.26         0.53        20.42        13.64         2.83 
TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 
       13.18         0.07         0.13        12.20         7.99         8.05 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6526 
       47.05        21.99        18.97        30.97        11.93        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT 
       10.26        15.22        10.55        12.33        18.21        14.27 
TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-EQ-5647 
       14.76        11.31        11.44         2.96         8.38         0.62 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 
       21.27        19.53         0.23        18.08        14.17         0.76 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 
       12.30        22.75         8.98        12.95        12.30         9.67 
TCGA-IN-8663 TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.39         7.82        60.56        20.15         8.52        61.25 
TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
        6.08       122.30       115.69        35.61        48.79         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS 
       46.26        22.19         2.70        17.85        23.41        13.35 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
       18.74        20.81        22.68         1.71         9.50        52.24 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6F 
        5.72        64.18        11.24        54.12 

$`AMP PEAK 19(9P13.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        9.30         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
        3.68        41.52        42.77        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.95         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        83.24        52.57        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO 
       12.33        25.25        10.52        12.00        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         8.02         7.59         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.02         5.29         3.42         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        30.71        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 
       26.70        11.70        19.56        11.01         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       18.05         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        35.24        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49        14.43        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        12.95        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21         1.12        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        8.22        10.68        12.56         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.51        12.89         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.66        19.36        13.51         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 
       20.02         3.02        27.02        15.95         1.02        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        22.98         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 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-D7-6815 
       18.84        18.54        18.61        17.85        13.35        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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 
       13.78        13.71        11.24         9.76        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         7.99        16.24        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       11.38         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.56         5.52        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 
       10.19         0.26         2.10        19.36        23.84         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV 
        8.94        16.87        19.04         5.79         0.92        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48         7.73        28.96        34.29        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       12.79         1.87         9.27        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
       61.22        36.16         7.36         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         4.54         6.58        21.04         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                        13.38                         12.59 
[1] "0.1 - 122.3 (13.4)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D19V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(9P13.3) MUTATED         3        5       16        5        10
  AMP PEAK 19(9P13.3) WILD-TYPE       8       14       32       27        67
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(9P13.3) MUTATED          13         9         23         16
  AMP PEAK 19(9P13.3) WILD-TYPE        71        20         74         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(9P13.3) MUTATED            6       11         1
  AMP PEAK 19(9P13.3) WILD-TYPE         42       40         3
D19V3, multiclass
            clus
vv           AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             5                            14
  STAGE IB                            16                            32
  STAGE II                             5                            27
  STAGE IIA                           10                            67
  STAGE IIB                           13                            71
  STAGE III                            9                            20
  STAGE IIIA                          23                            74
  STAGE IIIB                          16                            56
  STAGE IIIC                           6                            42
  STAGE IV                            11                            40
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 19(9P13.3) MUTATED      12  27  61  20
  AMP PEAK 19(9P13.3) WILD-TYPE    41  99 219 104
D19V4, multiclass
       clus
vv      AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  T0+T1                          12                            41
  T2                             27                            99
  T3                             61                           219
  T4                             20                           104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 19(9P13.3) MUTATED    37  43  18  21
  AMP PEAK 19(9P13.3) WILD-TYPE 163 139  78  76
D19V5, multiclass
    clus
vv   AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  N0                          37                           163
  N1                          43                           139
  N2                          18                            78
  N3                          21                            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"
D19V6, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED   106   7
  AMP PEAK 19(9P13.3) WILD-TYPE 407  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED    106    7
  AMP PEAK 19(9P13.3) WILD-TYPE  407   32
   clus
vv  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  0                         106                           407
  1                           7                            32
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED    36  88
  AMP PEAK 19(9P13.3) WILD-TYPE 146 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED     36   88
  AMP PEAK 19(9P13.3) WILD-TYPE  146  339
        clus
vv       AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  FEMALE                          36                           146
  MALE                            88                           339
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 19(9P13.3) MUTATED                                       9
  AMP PEAK 19(9P13.3) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(9P13.3) MUTATED                                                       25
  AMP PEAK 19(9P13.3) WILD-TYPE                                                    137
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(9P13.3) MUTATED                                                                  17
  AMP PEAK 19(9P13.3) WILD-TYPE                                                                64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 19(9P13.3) MUTATED                                                 23
  AMP PEAK 19(9P13.3) WILD-TYPE                                               55
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 19(9P13.3) MUTATED                                                          9
  AMP PEAK 19(9P13.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 19(9P13.3) MUTATED                                                           4
  AMP PEAK 19(9P13.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 19(9P13.3) MUTATED                                          3
  AMP PEAK 19(9P13.3) WILD-TYPE                                       10
D19V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 19(9P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  AMP PEAK 19(9P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED     3 121
  AMP PEAK 19(9P13.3) WILD-TYPE   3 482
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED      3  121
  AMP PEAK 19(9P13.3) WILD-TYPE    3  482
     clus
vv    AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  NO                            3                             3
  YES                         121                           482
[1] 2 2
[1] FALSE
D19V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 19(9P13.3) MUTATED    74   5   3   3
  AMP PEAK 19(9P13.3) WILD-TYPE 273  13  16  22
D19V11, multiclass
    clus
vv   AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  R0                          74                           273
  R1                           5                            13
  R2                           3                            16
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(9P13.3) MUTATED      25                         3
  AMP PEAK 19(9P13.3) WILD-TYPE   104                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(9P13.3) MUTATED                                           0    75
  AMP PEAK 19(9P13.3) WILD-TYPE                                         1   310
D19V13, multiclass
                                           clus
vv                                          AMP PEAK 19(9P13.3) MUTATED
  ASIAN                                                              25
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              75
                                           clus
vv                                          AMP PEAK 19(9P13.3) WILD-TYPE
  ASIAN                                                               104
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED     2  72
  AMP PEAK 19(9P13.3) WILD-TYPE   5 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED      2   72
  AMP PEAK 19(9P13.3) WILD-TYPE    5  322
                        clus
vv                       AMP PEAK 19(9P13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          72
                        clus
vv                       AMP PEAK 19(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           322
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(9Q34.3) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 20(9Q34.3) MUTATED   112  56
  AMP PEAK 20(9Q34.3) WILD-TYPE 242 165
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          168                           407 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                           56                           165 
$`AMP PEAK 20(9Q34.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-IC-A6RE TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS 
       31.27         5.92         7.69         0.53        12.82         9.96 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C 
       14.50       122.10        60.39         3.68        42.77        23.18 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OW 
        3.16         4.31         3.32         1.38        29.00         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NL TCGA-L5-A8NS 
        2.60         0.36         3.95        55.50        13.22        13.41 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O 
       27.12        46.09        10.36         5.92        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 
        0.10         0.10         0.10        12.49        12.59        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ 
       12.33         4.47        12.33        10.52        12.00        13.18 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-S8-A6BW 
        8.02        14.70        53.95         1.45        20.02        20.38 
TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 
        9.17         2.66         9.47         9.44         6.61        18.35 
TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 
       17.29        26.10        19.89         9.21        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 
       15.42        18.15        18.71        11.44         9.60         2.66 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 
        2.20         6.18        19.50        20.22        12.79        16.44 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       13.87        22.26         0.53         0.46        20.65        20.42 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 
       13.15        13.18         0.13         9.34        12.43         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       27.02         7.99        19.07        18.97        22.98        30.97 
TCGA-CG-5718 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
       36.00        12.66        11.93        17.19        15.22        10.55 
TCGA-D7-6820 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY 
       11.31        14.27        15.16        14.76        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 
        9.76         2.96        15.65         8.38         4.34         0.62 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       16.24        72.23        21.27         5.52        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP 
        1.51        14.17         0.76        12.30        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        6.25        12.30        27.42         3.45        18.81         3.39 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7O7 
        1.41        12.59         5.56        60.56        20.15        45.67 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 
       61.25         4.60        11.05       122.30       115.69        35.61 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PC 
       48.79         5.46        18.48        35.24        34.45        46.26 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       27.35        14.33        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D 
       36.16         9.50        52.24         9.04         5.72        64.18 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        40.08        54.12        21.11        12.43         0.79 

$`AMP PEAK 20(9Q34.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30        17.03         0.79        23.41        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       12.16        44.75        68.02        41.52        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         6.28        30.25         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93        18.35         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
        4.90         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02         2.66        35.97        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.55         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       52.57        10.45        12.66        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.59        12.76        22.39         0.10        15.52 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       13.22        25.25        12.23        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         7.82         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       28.11        11.24        15.91        10.16         3.42         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4184 
       19.73        26.70        11.70        19.56        11.01         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       12.76        17.49        14.43         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        12.95        16.31        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.51        12.89         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        19.36        13.51         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83         3.25         0.30         0.07         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-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         3.42        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        12.00         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 
       13.35        10.26        15.98        12.79        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       20.91        16.44         5.92        13.78        13.71        11.24 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 
        7.40         7.13         7.99        14.47        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       13.58         0.56         0.23         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         9.67         8.88         8.81        21.21 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         8.61         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       19.04         5.79         0.92        13.25        13.02        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W 
       65.16        36.69        11.70        11.93        61.22         7.36 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O 
        9.73         2.01        55.43         4.54         6.58        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        22.09        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        10.62 

  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                       122.30                        116.38 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                       13.165                        12.660 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.7)"
[1] "hr=" "1.4"
D20V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(9Q34.3) MUTATED         3        6       17        7        21
  AMP PEAK 20(9Q34.3) WILD-TYPE       8       13       31       25        56
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(9Q34.3) MUTATED          29         9         33         16
  AMP PEAK 20(9Q34.3) WILD-TYPE        55        20         64         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(9Q34.3) MUTATED           11       15         0
  AMP PEAK 20(9Q34.3) WILD-TYPE         37       36         4
D20V3, multiclass
            clus
vv           AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             6                            13
  STAGE IB                            17                            31
  STAGE II                             7                            25
  STAGE IIA                           21                            56
  STAGE IIB                           29                            55
  STAGE III                            9                            20
  STAGE IIIA                          33                            64
  STAGE IIIB                          16                            56
  STAGE IIIC                          11                            37
  STAGE IV                            15                            36
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 20(9Q34.3) MUTATED      14  42  86  29
  AMP PEAK 20(9Q34.3) WILD-TYPE    39  84 194  95
D20V4, multiclass
       clus
vv      AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  T0+T1                          14                            39
  T2                             42                            84
  T3                             86                           194
  T4                             29                            95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 20(9Q34.3) MUTATED    53  62  31  24
  AMP PEAK 20(9Q34.3) WILD-TYPE 147 120  65  73
D20V5, multiclass
    clus
vv   AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  N0                          53                           147
  N1                          62                           120
  N2                          31                            65
  N3                          24                            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"
D20V6, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED   154  10
  AMP PEAK 20(9Q34.3) WILD-TYPE 359  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED    154   10
  AMP PEAK 20(9Q34.3) WILD-TYPE  359   29
   clus
vv  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  0                         154                           359
  1                          10                            29
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED    44 136
  AMP PEAK 20(9Q34.3) WILD-TYPE 138 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED     44  136
  AMP PEAK 20(9Q34.3) WILD-TYPE  138  291
        clus
vv       AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  FEMALE                          44                           138
  MALE                           136                           291
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 20(9Q34.3) MUTATED                                      15
  AMP PEAK 20(9Q34.3) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(9Q34.3) MUTATED                                                       41
  AMP PEAK 20(9Q34.3) WILD-TYPE                                                    121
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(9Q34.3) MUTATED                                                                  19
  AMP PEAK 20(9Q34.3) WILD-TYPE                                                                62
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 20(9Q34.3) MUTATED                                                 27
  AMP PEAK 20(9Q34.3) WILD-TYPE                                               51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 20(9Q34.3) MUTATED                                                         10
  AMP PEAK 20(9Q34.3) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 20(9Q34.3) MUTATED                                                           4
  AMP PEAK 20(9Q34.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 20(9Q34.3) MUTATED                                          5
  AMP PEAK 20(9Q34.3) WILD-TYPE                                        8
D20V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 20(9Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  AMP PEAK 20(9Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED     3 177
  AMP PEAK 20(9Q34.3) WILD-TYPE   3 426
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED      3  177
  AMP PEAK 20(9Q34.3) WILD-TYPE    3  426
     clus
vv    AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  NO                            3                             3
  YES                         177                           426
[1] 2 2
[1] FALSE
D20V10, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 20(9Q34.3) MUTATED   101   6   2   7
  AMP PEAK 20(9Q34.3) WILD-TYPE 246  12  17  18
D20V11, multiclass
    clus
vv   AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  R0                         101                           246
  R1                           6                            12
  R2                           2                            17
  RX                           7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(9Q34.3) MUTATED      42                         4
  AMP PEAK 20(9Q34.3) WILD-TYPE    87                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 20(9Q34.3) MUTATED                                           0   108
  AMP PEAK 20(9Q34.3) WILD-TYPE                                         1   277
D20V13, multiclass
                                           clus
vv                                          AMP PEAK 20(9Q34.3) MUTATED
  ASIAN                                                              42
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             108
                                           clus
vv                                          AMP PEAK 20(9Q34.3) WILD-TYPE
  ASIAN                                                                87
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               277
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED     3 110
  AMP PEAK 20(9Q34.3) WILD-TYPE   4 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED      3  110
  AMP PEAK 20(9Q34.3) WILD-TYPE    4  284
                        clus
vv                       AMP PEAK 20(9Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         110
                        clus
vv                       AMP PEAK 20(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           284
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(10P11.22) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(10P11.22) MUTATED   100  59
  AMP PEAK 21(10P11.22) WILD-TYPE 254 162
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            159                             416 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                             59                             162 
$`AMP PEAK 21(10P11.22) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        58.55        16.24        32.45         7.69         6.21 
TCGA-IG-A3YB TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF 
        2.63         4.67       122.10        25.22         3.16         3.68 
TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE 
       32.61         3.16         7.43         2.60         3.02        55.50 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R 
       12.92        16.47         8.71        10.36        10.45         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.15        15.35        13.25        12.59        12.59         0.10 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.33        12.00        12.23         7.82         8.02         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EP 
        6.35        53.95        15.78        20.38         9.27        19.96 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE 
        1.55        18.31        42.87        46.19        10.16         2.10 
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 
        6.61        17.29        13.68         9.17        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 
       35.24        15.42        28.01        18.15        28.73         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 
        2.66         2.20        15.58         7.40         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 
       20.22        16.44         9.86        12.89         0.72        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
       13.51        20.65         1.15        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.16         9.34        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 
       20.02         4.01        47.05        21.99        12.00        30.97 
TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
        4.01        19.13        20.55        17.19        15.22        10.55 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       21.14        16.44        11.24        11.31        15.65         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
        0.62         7.99        72.23         3.48        19.53        17.06 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 
        0.23         1.51         5.92        14.17        11.41         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       12.30        24.20        22.75        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 
        6.25        12.95        23.84         9.67        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-MX-A663 
        3.39        18.38         6.74         6.51        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
       45.67        18.21         6.08        11.05         8.61        16.67 
TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
      122.30         5.46        21.73         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
       12.79        17.85        64.57        14.33        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94O 
       18.74        22.68         1.71         9.50         9.04        21.04 
TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-VQ-AA6J 
       22.09        16.14        21.11 

$`AMP PEAK 21(10P11.22) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30         7.63         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        4.21        33.27        20.09         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       30.25         0.30         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF 
        8.71        25.12         0.36         7.40         3.95         2.66 
TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49X 
        5.92        12.66        12.43        13.41         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.46        12.49        12.76        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       12.33        13.22         4.47        25.25        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6L4 
       13.18         0.13        33.11         5.16         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04        29.59         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.02         5.29         3.42         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81        22.82        12.43         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        18.18        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
       31.20        32.94        12.82        24.76        23.93        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56        12.95        16.31         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         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         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        8.98        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         3.42 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.31         6.58         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       15.95         1.02         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        11.93        18.84        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-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-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-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.44         9.76         2.96         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        7.13        16.24        14.47        21.27        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 
       18.08        26.47        14.27        12.59        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        11.84         3.25        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-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ 
       12.30         8.88         8.81        21.21        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        12.59         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       20.15         3.72        19.73         8.52        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        9.24         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        26.24        27.35        65.16        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22        20.81        36.16         7.36         9.73        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        2.66        42.54        11.24        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       32.94        29.98        17.13        54.12        26.04        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                         122.30                          116.38 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                          12.59                           12.79 
[1] "0.1 - 122.3 (12.6)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D21V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(10P11.22) MUTATED         5        9        9        5        20
  AMP PEAK 21(10P11.22) WILD-TYPE       6       10       39       27        57
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(10P11.22) MUTATED          25         9         27         23
  AMP PEAK 21(10P11.22) WILD-TYPE        59        20         70         49
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(10P11.22) MUTATED            8       15         2
  AMP PEAK 21(10P11.22) WILD-TYPE         40       36         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  STAGE I                                5                               6
  STAGE IA                               9                              10
  STAGE IB                               9                              39
  STAGE II                               5                              27
  STAGE IIA                             20                              57
  STAGE IIB                             25                              59
  STAGE III                              9                              20
  STAGE IIIA                            27                              70
  STAGE IIIB                            23                              49
  STAGE IIIC                             8                              40
  STAGE IV                              15                              36
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 21(10P11.22) MUTATED      19  26  84  30
  AMP PEAK 21(10P11.22) WILD-TYPE    34 100 196  94
D21V4, multiclass
       clus
vv      AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  T0+T1                            19                              34
  T2                               26                             100
  T3                               84                             196
  T4                               30                              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 21(10P11.22) MUTATED    55  51  26  25
  AMP PEAK 21(10P11.22) WILD-TYPE 145 131  70  72
D21V5, multiclass
    clus
vv   AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  N0                            55                             145
  N1                            51                             131
  N2                            26                              70
  N3                            25                              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"
D21V6, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED   136  12
  AMP PEAK 21(10P11.22) WILD-TYPE 377  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED    136   12
  AMP PEAK 21(10P11.22) WILD-TYPE  377   27
   clus
vv  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  0                           136                             377
  1                            12                              27
[1] 2 2
[1] FALSE
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED    47 119
  AMP PEAK 21(10P11.22) WILD-TYPE 135 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED     47  119
  AMP PEAK 21(10P11.22) WILD-TYPE  135  308
        clus
vv       AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  FEMALE                            47                             135
  MALE                             119                             308
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 21(10P11.22) MUTATED                                      14
  AMP PEAK 21(10P11.22) WILD-TYPE                                    57
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10P11.22) MUTATED                                                       42
  AMP PEAK 21(10P11.22) WILD-TYPE                                                    120
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(10P11.22) MUTATED                                                                  23
  AMP PEAK 21(10P11.22) WILD-TYPE                                                                58
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 21(10P11.22) MUTATED                                                 30
  AMP PEAK 21(10P11.22) WILD-TYPE                                               48
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 21(10P11.22) MUTATED                                                          4
  AMP PEAK 21(10P11.22) WILD-TYPE                                                       17
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 21(10P11.22) MUTATED                                                           1
  AMP PEAK 21(10P11.22) WILD-TYPE                                                         7
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 21(10P11.22) MUTATED                                          3
  AMP PEAK 21(10P11.22) WILD-TYPE                                       10
D21V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 21(10P11.22) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      3
                                                                   clus
vv                                                                  AMP PEAK 21(10P11.22) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED     3 163
  AMP PEAK 21(10P11.22) WILD-TYPE   3 440
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED      3  163
  AMP PEAK 21(10P11.22) WILD-TYPE    3  440
     clus
vv    AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  NO                              3                               3
  YES                           163                             440
[1] 2 2
[1] FALSE
D21V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(10P11.22) MUTATED    97   3   5   5
  AMP PEAK 21(10P11.22) WILD-TYPE 250  15  14  20
D21V11, multiclass
    clus
vv   AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  R0                            97                             250
  R1                             3                              15
  R2                             5                              14
  RX                             5                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(10P11.22) MUTATED      43                         6
  AMP PEAK 21(10P11.22) WILD-TYPE    86                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(10P11.22) MUTATED                                           1
  AMP PEAK 21(10P11.22) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 21(10P11.22) MUTATED      98
  AMP PEAK 21(10P11.22) WILD-TYPE   287
D21V13, multiclass
                                           clus
vv                                          AMP PEAK 21(10P11.22) MUTATED
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                98
                                           clus
vv                                          AMP PEAK 21(10P11.22) WILD-TYPE
  ASIAN                                                                  86
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED     1 111
  AMP PEAK 21(10P11.22) WILD-TYPE   6 283
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED      1  111
  AMP PEAK 21(10P11.22) WILD-TYPE    6  283
                        clus
vv                       AMP PEAK 21(10P11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       AMP PEAK 21(10P11.22) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             283
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(10Q22.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(10Q22.2) MUTATED    69  52
  AMP PEAK 22(10Q22.2) WILD-TYPE 285 169
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           121                            454 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                            52                            169 
$`AMP PEAK 22(10Q22.2) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FA 
       58.55         4.21         6.21         0.79       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OR 
        3.68        25.22         4.31         3.68        32.61         3.16 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ 
        3.02        55.50         2.66        12.92        16.47        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 
       10.45        13.41        13.15         0.10        13.25        12.76 
TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.23         8.02         7.59         5.06         6.35        53.95 
TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-ZR-A9CJ 
       15.78        20.38        22.82        42.87        10.16        19.73 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7197 
        6.61        18.35        17.29        19.33        26.10         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8286 
       35.24        15.42        18.15        14.43         0.69        12.95 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8682 
        2.66        15.58         7.40        14.04         9.21        16.44 
TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
        9.86        12.89         0.72        19.36        20.65         1.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4444 
       13.18         0.07         0.16         0.13        20.02        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 
       19.07        21.99        30.97        69.04        20.55        18.84 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
       10.55        12.33        18.21        16.44        11.24        11.31 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8238 
        9.76         7.40        16.24        72.23         0.56         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GU 
       11.41         0.76        12.30        24.20         8.98         6.25 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN 
       12.95         9.67        27.42         3.45         3.39        13.08 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
        6.44         1.81        18.21         9.24        11.05         8.61 
TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PM 
      122.30        35.61        21.73        46.26        12.79         1.87 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E 
       13.35        27.35        64.57        14.33        36.69        11.93 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94U 
       18.74        20.81         4.54         5.72        64.18        22.09 
TCGA-VQ-AA64 
       18.41 

$`AMP PEAK 22(10Q22.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        14.50        12.16        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00         4.70        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NK 
        0.36         7.40         3.95        35.97        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M 
       27.12        83.24        52.57        46.09         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43         0.10        15.35         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.00        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.82        14.70         7.04        29.59         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        46.19        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-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-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82        24.76        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        11.44        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 
        8.05         0.56        16.31         2.20         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        15.81        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         8.98        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         3.42         9.34        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        9.01        18.97         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 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
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-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.22        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        5.52         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-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-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84        12.30         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
       18.81        18.38         5.36         5.19         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51         5.56         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        45.67         8.52        61.25         6.08         4.60 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       35.24        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        16.31        22.19         2.50         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        23.41        15.65        26.24        65.16        11.70 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        52.24         9.04         2.01        55.43         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                        12.950                         12.605 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(10Q22.2) MUTATED         4        7        6        8         8
  AMP PEAK 22(10Q22.2) WILD-TYPE       7       12       42       24        69
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(10Q22.2) MUTATED          15         8         24         16
  AMP PEAK 22(10Q22.2) WILD-TYPE        69        21         73         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(10Q22.2) MUTATED            8       11         2
  AMP PEAK 22(10Q22.2) WILD-TYPE         40       40         2
D22V3, multiclass
            clus
vv           AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              7                             12
  STAGE IB                              6                             42
  STAGE II                              8                             24
  STAGE IIA                             8                             69
  STAGE IIB                            15                             69
  STAGE III                             8                             21
  STAGE IIIA                           24                             73
  STAGE IIIB                           16                             56
  STAGE IIIC                            8                             40
  STAGE IV                             11                             40
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 22(10Q22.2) MUTATED      16  20  59  23
  AMP PEAK 22(10Q22.2) WILD-TYPE    37 106 221 101
D22V4, multiclass
       clus
vv      AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  T0+T1                           16                             37
  T2                              20                            106
  T3                              59                            221
  T4                              23                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 22(10Q22.2) MUTATED    39  34  24  21
  AMP PEAK 22(10Q22.2) WILD-TYPE 161 148  72  76
D22V5, multiclass
    clus
vv   AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  N0                           39                            161
  N1                           34                            148
  N2                           24                             72
  N3                           21                             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"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED   103   6
  AMP PEAK 22(10Q22.2) WILD-TYPE 410  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED    103    6
  AMP PEAK 22(10Q22.2) WILD-TYPE  410   33
   clus
vv  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  0                          103                            410
  1                            6                             33
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED    35  89
  AMP PEAK 22(10Q22.2) WILD-TYPE 147 338
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED     35   89
  AMP PEAK 22(10Q22.2) WILD-TYPE  147  338
        clus
vv       AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  FEMALE                           35                            147
  MALE                             89                            338
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 22(10Q22.2) MUTATED                                      12
  AMP PEAK 22(10Q22.2) WILD-TYPE                                    59
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(10Q22.2) MUTATED                                                       28
  AMP PEAK 22(10Q22.2) WILD-TYPE                                                    134
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(10Q22.2) MUTATED                                                                  18
  AMP PEAK 22(10Q22.2) WILD-TYPE                                                                63
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 22(10Q22.2) MUTATED                                                 21
  AMP PEAK 22(10Q22.2) WILD-TYPE                                               57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 22(10Q22.2) MUTATED                                                          4
  AMP PEAK 22(10Q22.2) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 22(10Q22.2) MUTATED                                                           2
  AMP PEAK 22(10Q22.2) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 22(10Q22.2) MUTATED                                          3
  AMP PEAK 22(10Q22.2) WILD-TYPE                                       10
D22V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 22(10Q22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 22(10Q22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED     2 122
  AMP PEAK 22(10Q22.2) WILD-TYPE   4 481
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED      2  122
  AMP PEAK 22(10Q22.2) WILD-TYPE    4  481
     clus
vv    AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  NO                             2                              4
  YES                          122                            481
[1] 2 2
[1] FALSE
D22V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(10Q22.2) MUTATED    77   1   3   4
  AMP PEAK 22(10Q22.2) WILD-TYPE 270  17  16  21
D22V11, multiclass
    clus
vv   AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  R0                           77                            270
  R1                            1                             17
  R2                            3                             16
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(10Q22.2) MUTATED      28                         1
  AMP PEAK 22(10Q22.2) WILD-TYPE   101                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(10Q22.2) MUTATED                                           1
  AMP PEAK 22(10Q22.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 22(10Q22.2) MUTATED      82
  AMP PEAK 22(10Q22.2) WILD-TYPE   303
D22V13, multiclass
                                           clus
vv                                          AMP PEAK 22(10Q22.2) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               82
                                           clus
vv                                          AMP PEAK 22(10Q22.2) WILD-TYPE
  ASIAN                                                                101
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED     0  82
  AMP PEAK 22(10Q22.2) WILD-TYPE   7 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED      0   82
  AMP PEAK 22(10Q22.2) WILD-TYPE    7  312
                        clus
vv                       AMP PEAK 22(10Q22.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       AMP PEAK 22(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            312
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(10Q26.13) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(10Q26.13) MUTATED    67  48
  AMP PEAK 23(10Q26.13) WILD-TYPE 287 173
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            115                             460 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                             48                             173 
$`AMP PEAK 23(10Q26.13) MUTATED`
TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6F8 
       58.55         7.69         6.21        18.64         0.79       122.10 
TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OR 
        3.68        25.22         4.31         3.68         3.32         3.16 
TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ 
        2.60         3.02        55.50         2.66        16.47        10.36 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A3 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
       13.15         0.10        12.76         7.59         5.06         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-X8-AAAR 
       53.95        15.78         2.89        22.82        42.87        10.16 
TCGA-ZR-A9CJ TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 
       19.73         6.61         4.64        18.35        17.29        13.68 
TCGA-BR-6564 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       26.10        31.20         9.21        35.24        15.42        28.01 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 
        0.69         9.60        12.95         2.66        15.58         7.40 
TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8525 
       16.44         0.72        19.36         1.15        13.18         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4443 
        0.07         0.16         0.13        20.02        27.02        29.98 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5730 
       19.07         7.07        12.00        30.97        36.00         4.01 
TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 
       69.04        20.55        18.84        17.19        15.22        10.55 
TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       16.80        14.27        16.44        11.24        11.31         9.76 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 TCGA-HU-8238 
        0.62         7.99        72.23         3.48        17.06         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GY TCGA-HU-A4H5 
       11.41         0.76        12.30        24.20         0.26        12.30 
TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-R5-A7ZE 
        9.67         3.39        18.38         6.44         5.56        18.21 
TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8PC 
        6.08        11.05         5.46        18.48        21.73        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       12.79        64.57        14.33        11.93        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94U 
       22.68         9.73         4.54         5.72        64.18        22.09 
TCGA-VQ-AA64 
       18.41 

$`AMP PEAK 23(10Q26.13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85        20.78         2.63        20.12         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        0.53        17.03        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        14.50        12.16        44.75        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
       24.00         4.70        32.61        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y 
        7.13         7.43         6.94         8.71        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        7.40         3.95        35.97        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
       27.12        83.24        52.57        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
       12.66        12.43        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG 
       14.70         7.04        29.59         9.30         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.10         2.66        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        9.47         9.44         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        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       12.16         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        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       11.44        12.26        20.55         8.05         0.56        16.31 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        15.81         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62         3.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       54.08         4.01        14.01        47.05        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5719 
        0.00         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        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        7.13        16.24        14.47        21.27        11.38        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        5.52         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        23.84         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42        21.21         3.45        18.81         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81         7.82        13.51         2.53        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       61.25         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79        13.25        13.02        35.24        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19         2.50         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ 
       23.41        15.65        13.35        26.24        27.35        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       36.69        11.70        61.22         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50        52.24         9.04         2.01        55.43         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        11.24        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                          122.1                           122.3 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                          12.30                           12.79 
[1] "0.1 - 122.1 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(10Q26.13) MUTATED         4        8        8        8         7
  AMP PEAK 23(10Q26.13) WILD-TYPE       7       11       40       24        70
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(10Q26.13) MUTATED          15         6         24         10
  AMP PEAK 23(10Q26.13) WILD-TYPE        69        23         73         62
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(10Q26.13) MUTATED            8       10         2
  AMP PEAK 23(10Q26.13) WILD-TYPE         40       41         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  STAGE I                                4                               7
  STAGE IA                               8                              11
  STAGE IB                               8                              40
  STAGE II                               8                              24
  STAGE IIA                              7                              70
  STAGE IIB                             15                              69
  STAGE III                              6                              23
  STAGE IIIA                            24                              73
  STAGE IIIB                            10                              62
  STAGE IIIC                             8                              40
  STAGE IV                              10                              41
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 23(10Q26.13) MUTATED      16  22  54  19
  AMP PEAK 23(10Q26.13) WILD-TYPE    37 104 226 105
D23V4, multiclass
       clus
vv      AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  T0+T1                            16                              37
  T2                               22                             104
  T3                               54                             226
  T4                               19                             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 23(10Q26.13) MUTATED    38  33  21  18
  AMP PEAK 23(10Q26.13) WILD-TYPE 162 149  75  79
D23V5, multiclass
    clus
vv   AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  N0                            38                             162
  N1                            33                             149
  N2                            21                              75
  N3                            18                              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"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED    98   5
  AMP PEAK 23(10Q26.13) WILD-TYPE 415  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED     98    5
  AMP PEAK 23(10Q26.13) WILD-TYPE  415   34
   clus
vv  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  0                            98                             415
  1                             5                              34
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED    36  83
  AMP PEAK 23(10Q26.13) WILD-TYPE 146 344
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED     36   83
  AMP PEAK 23(10Q26.13) WILD-TYPE  146  344
        clus
vv       AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  FEMALE                            36                             146
  MALE                              83                             344
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 23(10Q26.13) MUTATED                                       9
  AMP PEAK 23(10Q26.13) WILD-TYPE                                    62
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(10Q26.13) MUTATED                                                       29
  AMP PEAK 23(10Q26.13) WILD-TYPE                                                    133
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(10Q26.13) MUTATED                                                                  18
  AMP PEAK 23(10Q26.13) WILD-TYPE                                                                63
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 23(10Q26.13) MUTATED                                                 21
  AMP PEAK 23(10Q26.13) WILD-TYPE                                               57
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 23(10Q26.13) MUTATED                                                          5
  AMP PEAK 23(10Q26.13) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 23(10Q26.13) MUTATED                                                           3
  AMP PEAK 23(10Q26.13) WILD-TYPE                                                         5
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 23(10Q26.13) MUTATED                                          2
  AMP PEAK 23(10Q26.13) WILD-TYPE                                       11
D23V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 23(10Q26.13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  AMP PEAK 23(10Q26.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED     2 117
  AMP PEAK 23(10Q26.13) WILD-TYPE   4 486
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED      2  117
  AMP PEAK 23(10Q26.13) WILD-TYPE    4  486
     clus
vv    AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  NO                              2                               4
  YES                           117                             486
[1] 2 2
[1] FALSE
D23V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(10Q26.13) MUTATED    73   2   4   6
  AMP PEAK 23(10Q26.13) WILD-TYPE 274  16  15  19
D23V11, multiclass
    clus
vv   AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  R0                            73                             274
  R1                             2                              16
  R2                             4                              15
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(10Q26.13) MUTATED      19                         5
  AMP PEAK 23(10Q26.13) WILD-TYPE   110                         8
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(10Q26.13) MUTATED                                           0
  AMP PEAK 23(10Q26.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 23(10Q26.13) MUTATED      79
  AMP PEAK 23(10Q26.13) WILD-TYPE   306
D23V13, multiclass
                                           clus
vv                                          AMP PEAK 23(10Q26.13) MUTATED
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                79
                                           clus
vv                                          AMP PEAK 23(10Q26.13) WILD-TYPE
  ASIAN                                                                 110
  BLACK OR AFRICAN AMERICAN                                               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED     0  75
  AMP PEAK 23(10Q26.13) WILD-TYPE   7 319
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED      0   75
  AMP PEAK 23(10Q26.13) WILD-TYPE    7  319
                        clus
vv                       AMP PEAK 23(10Q26.13) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            75
                        clus
vv                       AMP PEAK 23(10Q26.13) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             319
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(11P13) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(11P13) MUTATED    63  60
  AMP PEAK 24(11P13) WILD-TYPE 291 161
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         123                          452 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                          60                          161 
$`AMP PEAK 24(11P13) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A8O2 TCGA-IG-A97H 
        7.63         8.94        16.24         0.53         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OH 
      122.10         3.68        25.22         8.94        24.00        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF 
       47.93        18.35         4.90        29.00         6.94         2.66 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S 
        5.49        27.12        52.57        46.09         5.92        13.15 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        12.59        22.39        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       10.52        12.00        12.03         7.82         7.59         7.04 
TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX 
        7.00         3.42        22.82        12.43        18.31        28.11 
TCGA-VR-A8EZ TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6455 
       18.18        19.73        11.70        11.01         9.44        13.87 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 
       17.29        19.33        26.10        18.15         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8590 
        0.69         9.60        15.58         7.40         9.21         9.34 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IY 
       11.54        15.68        12.56         6.08        22.26        12.89 
TCGA-BR-A4J2 TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 
       14.17        13.51         0.07         0.10         0.16         0.13 
TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4472 
        9.34        12.20        20.02        54.08        19.07        12.00 
TCGA-CG-5717 TCGA-CG-5722 TCGA-D7-6822 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-8122 
        6.97         0.99        12.33        14.66         0.62         7.99 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 
       14.07        17.06         0.56         0.23         5.92        14.17 
TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO 
       24.30        27.42         3.45        18.38         5.36         1.41 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI 
        5.56         1.81         5.56        37.64        18.21        61.25 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        8.61        16.67       115.69        57.44         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX 
       18.48        35.24        22.19         2.70        27.35        64.57 
TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94U 
       22.68         9.50         9.73         9.04         4.54        22.09 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6K 
       29.98        54.12        12.43 

$`AMP PEAK 24(11P13) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
       42.77        25.41        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
        6.28         3.16        30.25         0.30         4.31         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        4.70        19.99        21.01         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        3.16        58.59         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
        7.76        21.37         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX 
        0.10        15.52        11.54        12.33        25.25        12.23 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
       13.18         0.13        33.11         5.16         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45        12.69        20.02        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55         8.12        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
        2.66        26.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 
        6.61        34.68        15.95        13.68        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.66        16.31         2.20         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79        15.81        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       15.81        16.44         9.86         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        7.53         1.48        13.41        13.51         8.98         0.72 
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-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-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         3.42        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         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-4444 
        7.99         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44         9.76         2.96        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.40         7.13        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         5.52        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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       21.21        18.81         3.39         5.19        13.08         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59         6.51         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       60.56        20.15         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
      122.30        37.91        40.64       116.38        71.38         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        20.81         1.71        36.16         7.36 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       52.24         2.01        55.43         6.58         5.72        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        32.94        17.13        26.04        16.14        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                        0.07                         0.00 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                       122.1                        122.3 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                       12.33                        12.82 
[1] "0.1 - 122.1 (12.3)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.4"
D24V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(11P13) MUTATED         3        3        8        4        15
  AMP PEAK 24(11P13) WILD-TYPE       8       16       40       28        62
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(11P13) MUTATED          19         9         19         13
  AMP PEAK 24(11P13) WILD-TYPE        65        20         78         59
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(11P13) MUTATED           13       16         3
  AMP PEAK 24(11P13) WILD-TYPE         35       35         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  STAGE I                             3                            8
  STAGE IA                            3                           16
  STAGE IB                            8                           40
  STAGE II                            4                           28
  STAGE IIA                          15                           62
  STAGE IIB                          19                           65
  STAGE III                           9                           20
  STAGE IIIA                         19                           78
  STAGE IIIB                         13                           59
  STAGE IIIC                         13                           35
  STAGE IV                           16                           35
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 24(11P13) MUTATED      12  15  68  32
  AMP PEAK 24(11P13) WILD-TYPE    41 111 212  92
D24V4, multiclass
       clus
vv      AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  T0+T1                         12                           41
  T2                            15                          111
  T3                            68                          212
  T4                            32                           92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 24(11P13) MUTATED    35  44  25  20
  AMP PEAK 24(11P13) WILD-TYPE 165 138  71  77
D24V5, multiclass
    clus
vv   AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  N0                         35                          165
  N1                         44                          138
  N2                         25                           71
  N3                         20                           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"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED   105  13
  AMP PEAK 24(11P13) WILD-TYPE 408  26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED    105   13
  AMP PEAK 24(11P13) WILD-TYPE  408   26
   clus
vv  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  0                        105                          408
  1                         13                           26
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED    30 103
  AMP PEAK 24(11P13) WILD-TYPE 152 324
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED     30  103
  AMP PEAK 24(11P13) WILD-TYPE  152  324
        clus
vv       AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  FEMALE                         30                          152
  MALE                          103                          324
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 24(11P13) MUTATED                                      13
  AMP PEAK 24(11P13) WILD-TYPE                                    58
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11P13) MUTATED                                                       32
  AMP PEAK 24(11P13) WILD-TYPE                                                    130
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(11P13) MUTATED                                                                  14
  AMP PEAK 24(11P13) WILD-TYPE                                                                67
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 24(11P13) MUTATED                                                 17
  AMP PEAK 24(11P13) WILD-TYPE                                               61
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 24(11P13) MUTATED                                                          5
  AMP PEAK 24(11P13) WILD-TYPE                                                       16
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 24(11P13) MUTATED                                                           0
  AMP PEAK 24(11P13) WILD-TYPE                                                         8
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 24(11P13) MUTATED                                          5
  AMP PEAK 24(11P13) WILD-TYPE                                        8
D24V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 24(11P13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   5
                                                                   clus
vv                                                                  AMP PEAK 24(11P13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED     2 131
  AMP PEAK 24(11P13) WILD-TYPE   4 472
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED      2  131
  AMP PEAK 24(11P13) WILD-TYPE    4  472
     clus
vv    AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  NO                           2                            4
  YES                        131                          472
[1] 2 2
[1] FALSE
D24V10, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 24(11P13) MUTATED    64   4   7   5
  AMP PEAK 24(11P13) WILD-TYPE 283  14  12  20
D24V11, multiclass
    clus
vv   AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  R0                         64                          283
  R1                          4                           14
  R2                          7                           12
  RX                          5                           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(11P13) MUTATED      34                         4
  AMP PEAK 24(11P13) WILD-TYPE    95                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 24(11P13) MUTATED                                           1    76
  AMP PEAK 24(11P13) WILD-TYPE                                         0   309
D24V13, multiclass
                                           clus
vv                                          AMP PEAK 24(11P13) MUTATED
  ASIAN                                                             34
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             76
                                           clus
vv                                          AMP PEAK 24(11P13) WILD-TYPE
  ASIAN                                                               95
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              309
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED     1  81
  AMP PEAK 24(11P13) WILD-TYPE   6 313
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED      1   81
  AMP PEAK 24(11P13) WILD-TYPE    6  313
                        clus
vv                       AMP PEAK 24(11P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         81
                        clus
vv                       AMP PEAK 24(11P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          313
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(11Q13.3) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(11Q13.3) MUTATED   121  74
  AMP PEAK 25(11Q13.3) WILD-TYPE 233 147
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           195                            380 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                            74                            147 
$`AMP PEAK 25(11Q13.3) MUTATED`
TCGA-2H-A9GN TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        8.94        33.27         0.85        20.78        20.12        18.64 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       17.03        23.41         9.96         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43H 
      122.10        60.39         3.68        25.41        25.22         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        4.31         8.94        24.00         3.68         4.70        32.61 
TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V 
       47.93         1.38        58.59        29.00         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.95        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55         5.49        21.37         8.71        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W 
        5.92        12.66        12.43         0.10        13.15        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       25.25        12.00        12.23        12.03        13.18         0.13 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.82         8.02         7.59         7.04         6.35        53.95 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ 
       15.78         7.00         3.42         9.27        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       46.19        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6455 
        2.10         2.66        19.73        11.01         9.44        13.87 
TCGA-BR-6457 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8077 
       13.68        35.24        18.15         3.45        17.49         0.69 
TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8485 TCGA-BR-8589 
        9.60        15.58        19.50        17.52         9.21        15.81 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       11.54        15.68         8.22        22.26         1.48        12.89 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8532 
        1.15        13.64         3.25         0.07         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        0.13         0.13         9.34        11.61        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5722 
       54.08        47.05        19.07        12.03        12.00         0.99 
TCGA-CG-5724 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.03        18.21        14.66        11.24         2.96        15.65 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8610 
        7.99        72.23        17.06         0.56         5.92         0.76 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       24.30         3.25         0.26        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       27.42         3.39         5.36         5.19         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        6.74         5.56         1.81         5.56        37.64         9.86 
TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 
       61.25         8.61        16.67       122.30       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        35.61        19.04         5.46        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       35.24        22.19         2.70        27.35        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Y 
       36.69        11.93        18.74        22.68         1.71         9.73 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        4.54        64.18        11.24        40.08        32.94        29.98 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       21.11        12.43         0.79 

$`AMP PEAK 25(11Q13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.09         2.63         3.88         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.82        14.86        44.75        68.02        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25        19.99        21.01        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W 
        3.16         4.90         7.13         7.43         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        7.40         3.02        35.97        16.47        13.22         7.76 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O 
       13.41        27.12        83.24        10.36        10.45        13.41 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-M9-A5M8 
       15.35         0.10        11.54         4.47        10.52        33.11 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.16         5.06        14.70        29.59         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        1.45        12.69        20.02        20.38         5.29         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-X8-AAAR 
       15.35         4.44        19.96         1.55        42.87        10.16 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        17.29        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        12.26        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66        16.31         2.20         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         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        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         9.86        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        7.53         6.08        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 
        0.07         0.13         0.16         0.10         0.10         3.42 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.31        12.43         6.58         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62        16.24        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
        6.25        10.19         2.10        12.95        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN 
        8.81        21.21         3.45        18.81        18.38        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
       12.59         6.51         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       20.15         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW 
        6.08         4.60         9.24        11.05         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       40.64       116.38        71.38        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       48.79        13.25        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q 
       13.35        26.24        65.16        11.70        61.22        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       36.16         7.36         9.50        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       22.09        18.41        28.41        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        10.62 

  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                         12.43                          12.95 
[1] "0.1 - 122.3 (12.4)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1"  
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(11Q13.3) MUTATED         5        5       12        9        31
  AMP PEAK 25(11Q13.3) WILD-TYPE       6       14       36       23        46
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(11Q13.3) MUTATED          27        16         30         23
  AMP PEAK 25(11Q13.3) WILD-TYPE        57        13         67         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(11Q13.3) MUTATED           18       15         3
  AMP PEAK 25(11Q13.3) WILD-TYPE         30       36         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              5                             14
  STAGE IB                             12                             36
  STAGE II                              9                             23
  STAGE IIA                            31                             46
  STAGE IIB                            27                             57
  STAGE III                            16                             13
  STAGE IIIA                           30                             67
  STAGE IIIB                           23                             49
  STAGE IIIC                           18                             30
  STAGE IV                             15                             36
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 25(11Q13.3) MUTATED      20  42  95  41
  AMP PEAK 25(11Q13.3) WILD-TYPE    33  84 185  83
D25V4, multiclass
       clus
vv      AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  T0+T1                           20                             33
  T2                              42                             84
  T3                              95                            185
  T4                              41                             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 25(11Q13.3) MUTATED    69  64  38  24
  AMP PEAK 25(11Q13.3) WILD-TYPE 131 118  58  73
D25V5, multiclass
    clus
vv   AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  N0                           69                            131
  N1                           64                            118
  N2                           38                             58
  N3                           24                             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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED   176  11
  AMP PEAK 25(11Q13.3) WILD-TYPE 337  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED    176   11
  AMP PEAK 25(11Q13.3) WILD-TYPE  337   28
   clus
vv  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  0                          176                            337
  1                           11                             28
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED    51 158
  AMP PEAK 25(11Q13.3) WILD-TYPE 131 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED     51  158
  AMP PEAK 25(11Q13.3) WILD-TYPE  131  269
        clus
vv       AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  FEMALE                           51                            131
  MALE                            158                            269
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 25(11Q13.3) MUTATED                                      14
  AMP PEAK 25(11Q13.3) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(11Q13.3) MUTATED                                                       45
  AMP PEAK 25(11Q13.3) WILD-TYPE                                                    117
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(11Q13.3) MUTATED                                                                  21
  AMP PEAK 25(11Q13.3) WILD-TYPE                                                                60
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 25(11Q13.3) MUTATED                                                 24
  AMP PEAK 25(11Q13.3) WILD-TYPE                                               54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 25(11Q13.3) MUTATED                                                          7
  AMP PEAK 25(11Q13.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 25(11Q13.3) MUTATED                                                           1
  AMP PEAK 25(11Q13.3) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 25(11Q13.3) MUTATED                                          2
  AMP PEAK 25(11Q13.3) WILD-TYPE                                       11
D25V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 25(11Q13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 25(11Q13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       117
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED     2 207
  AMP PEAK 25(11Q13.3) WILD-TYPE   4 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED      2  207
  AMP PEAK 25(11Q13.3) WILD-TYPE    4  396
     clus
vv    AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  NO                             2                              4
  YES                          207                            396
[1] 2 2
[1] FALSE
D25V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(11Q13.3) MUTATED    91   5   7   6
  AMP PEAK 25(11Q13.3) WILD-TYPE 256  13  12  19
D25V11, multiclass
    clus
vv   AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  R0                           91                            256
  R1                            5                             13
  R2                            7                             12
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(11Q13.3) MUTATED      54                         6
  AMP PEAK 25(11Q13.3) WILD-TYPE    75                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(11Q13.3) MUTATED                                           1
  AMP PEAK 25(11Q13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 25(11Q13.3) MUTATED     125
  AMP PEAK 25(11Q13.3) WILD-TYPE   260
D25V13, multiclass
                                           clus
vv                                          AMP PEAK 25(11Q13.3) MUTATED
  ASIAN                                                               54
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              125
                                           clus
vv                                          AMP PEAK 25(11Q13.3) WILD-TYPE
  ASIAN                                                                 75
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED     1 126
  AMP PEAK 25(11Q13.3) WILD-TYPE   6 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED      1  126
  AMP PEAK 25(11Q13.3) WILD-TYPE    6  268
                        clus
vv                       AMP PEAK 25(11Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK 25(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            268
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(12P12.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(12P12.1) MUTATED   117  75
  AMP PEAK 26(12P12.1) WILD-TYPE 237 146
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           192                            383 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                            75                            146 
$`AMP PEAK 26(12P12.1) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         5.92        16.24         4.21        32.45        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 
        2.63        20.12        18.64         3.88         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A93D TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       14.50        31.56         0.30         4.31        24.00        19.99 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
       47.93        18.35         3.32         4.90        29.00         6.94 
TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NT 
        0.36         2.66        16.47        13.22        21.37        27.12 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 
        0.10        13.15         0.10        13.25        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.59         0.10        15.52        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       25.25        10.52        12.00        13.18         0.13         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG 
        7.59         5.06        29.59         6.35        53.95        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       20.02        20.38        19.96         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       28.11        18.18        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 
       19.73         9.47         6.61        39.12        32.78        25.61 
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8078 
       12.16        21.11        28.73         3.45        18.71        12.26 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        2.20         7.40        19.50        13.08         0.26         0.95 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 
       14.04         3.32         0.26        20.22        15.81        11.54 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J2 
        8.22         7.53        22.26         1.48         0.72        14.17 
TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 
        1.15         2.83         3.25         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 
        0.07         0.16         0.10        12.43        11.61        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 
       47.05        21.99        12.00         0.99        12.03        79.07 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 
       12.66        19.13        20.55        18.54        17.19        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YV TCGA-D7-A6EX TCGA-D7-A6F0 
       11.31        19.50        18.21         5.92        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A72C 
       15.65         8.38         7.40         0.62        16.24        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 
        3.48        19.53        22.29         5.52         1.51        14.17 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP 
       12.10        24.30         3.25        22.75        25.81         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
        6.51         6.25        10.19         8.81        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU 
        3.39         5.36         6.44         6.74         6.51         1.81 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI 
        7.82         2.53        60.56        37.64        18.21        61.25 
TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL 
        6.08        11.05        16.67         8.94         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       48.79        13.25        18.48        35.24        21.73         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N 
       22.19        17.85        14.33        36.69        11.93        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA6K 
       20.81        36.16         4.54         5.72        11.24        12.43 

$`AMP PEAK 26(12P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QT 
        7.69         6.21        33.27         0.85        20.78         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.70        32.61        21.01         7.17         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       58.59         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH 
        7.40         3.95         3.02        55.50        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        13.55         7.76         5.49         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       83.24        52.57        12.43        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HX TCGA-LN-A7HY 
       12.49        22.39        11.54        12.33        12.23        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 
       33.11         5.16         7.82        14.70         7.04         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89         1.45         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       12.43        30.71        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.17        15.91        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 
       17.29        13.68        19.33        26.10         9.17        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        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-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32        12.43         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44         0.69         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 
        0.56        12.95         2.66        16.31        15.58         6.18 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
       22.19        17.52        26.33         4.31        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       14.79        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.49        15.81        16.44         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        8.98         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-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.15        13.18         0.07         0.07         0.10         0.13 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.31         6.58        12.20         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
       36.00         1.02         0.99         6.02       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.36        11.93        18.84        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.22        15.98        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        17.19        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       11.44         9.76         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       72.23        21.27        14.07        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.27        12.59        11.41        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         0.26         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI 
       12.30         9.67         8.88        21.21        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X 
        5.19        13.08         1.41        12.59         5.56        13.51 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        20.15         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        8.52         4.60         9.24         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E7 
       35.61        16.87        19.04         5.46        13.02        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       15.65        13.35        26.24        27.35        64.57        65.16 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70        61.22        22.68         1.71         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.73        52.24         9.04         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
       64.18        21.04         2.66        42.54        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         0.79 

  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                        12.065                         13.150 
[1] "0.1 - 79.1 (12.1)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(12P12.1) MUTATED         0        3       13        8        35
  AMP PEAK 26(12P12.1) WILD-TYPE      11       16       35       24        42
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(12P12.1) MUTATED          25        12         36         24
  AMP PEAK 26(12P12.1) WILD-TYPE        59        17         61         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(12P12.1) MUTATED           17       15         3
  AMP PEAK 26(12P12.1) WILD-TYPE         31       36         1
D26V3, multiclass
            clus
vv           AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  STAGE I                               0                             11
  STAGE IA                              3                             16
  STAGE IB                             13                             35
  STAGE II                              8                             24
  STAGE IIA                            35                             42
  STAGE IIB                            25                             59
  STAGE III                            12                             17
  STAGE IIIA                           36                             61
  STAGE IIIB                           24                             48
  STAGE IIIC                           17                             31
  STAGE IV                             15                             36
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 26(12P12.1) MUTATED      12  37 115  29
  AMP PEAK 26(12P12.1) WILD-TYPE    41  89 165  95
D26V4, multiclass
       clus
vv      AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  T0+T1                           12                             41
  T2                              37                             89
  T3                             115                            165
  T4                              29                             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 26(12P12.1) MUTATED    64  60  36  32
  AMP PEAK 26(12P12.1) WILD-TYPE 136 122  60  65
D26V5, multiclass
    clus
vv   AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  N0                           64                            136
  N1                           60                            122
  N2                           36                             60
  N3                           32                             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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED   164  14
  AMP PEAK 26(12P12.1) WILD-TYPE 349  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED    164   14
  AMP PEAK 26(12P12.1) WILD-TYPE  349   25
   clus
vv  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  0                          164                            349
  1                           14                             25
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED    49 152
  AMP PEAK 26(12P12.1) WILD-TYPE 133 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED     49  152
  AMP PEAK 26(12P12.1) WILD-TYPE  133  275
        clus
vv       AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  FEMALE                           49                            133
  MALE                            152                            275
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 26(12P12.1) MUTATED                                      24
  AMP PEAK 26(12P12.1) WILD-TYPE                                    47
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12P12.1) MUTATED                                                       48
  AMP PEAK 26(12P12.1) WILD-TYPE                                                    114
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(12P12.1) MUTATED                                                                  17
  AMP PEAK 26(12P12.1) WILD-TYPE                                                                64
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 26(12P12.1) MUTATED                                                 29
  AMP PEAK 26(12P12.1) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 26(12P12.1) MUTATED                                                          5
  AMP PEAK 26(12P12.1) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 26(12P12.1) MUTATED                                                           1
  AMP PEAK 26(12P12.1) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 26(12P12.1) MUTATED                                          2
  AMP PEAK 26(12P12.1) WILD-TYPE                                       11
D26V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 26(12P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 26(12P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED     2 199
  AMP PEAK 26(12P12.1) WILD-TYPE   4 404
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED      2  199
  AMP PEAK 26(12P12.1) WILD-TYPE    4  404
     clus
vv    AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  NO                             2                              4
  YES                          199                            404
[1] 2 2
[1] FALSE
D26V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(12P12.1) MUTATED   102   6   6   4
  AMP PEAK 26(12P12.1) WILD-TYPE 245  12  13  21
D26V11, multiclass
    clus
vv   AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  R0                          102                            245
  R1                            6                             12
  R2                            6                             13
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(12P12.1) MUTATED      54                         3
  AMP PEAK 26(12P12.1) WILD-TYPE    75                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 26(12P12.1) MUTATED                                           0
  AMP PEAK 26(12P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 26(12P12.1) MUTATED     123
  AMP PEAK 26(12P12.1) WILD-TYPE   262
D26V13, multiclass
                                           clus
vv                                          AMP PEAK 26(12P12.1) MUTATED
  ASIAN                                                               54
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              123
                                           clus
vv                                          AMP PEAK 26(12P12.1) WILD-TYPE
  ASIAN                                                                 75
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                262
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED     3 138
  AMP PEAK 26(12P12.1) WILD-TYPE   4 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED      3  138
  AMP PEAK 26(12P12.1) WILD-TYPE    4  256
                        clus
vv                       AMP PEAK 26(12P12.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          138
                        clus
vv                       AMP PEAK 26(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(12Q15) MUTATION ANALYSIS
D27V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 27(12Q15) MUTATED    89  64
  AMP PEAK 27(12Q15) WILD-TYPE 265 157
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         153                          422 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                          64                          157 
$`AMP PEAK 27(12Q15) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A43J 
        7.63        16.24        32.45         0.53         4.67         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88S 
        8.94        24.00        47.93         3.32         4.90         6.94 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NT 
       55.50         2.66        13.48        13.22         5.49        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W 
       52.57        46.09        10.36        10.45         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        12.59         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG 
        4.47         0.13         7.59        29.59         6.35        12.69 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EZ 
       20.38         3.42        19.96         1.55        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TK 
       42.87        11.24        10.16         2.10        19.73         9.47 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6801 
        6.61        18.35         6.18        39.12        32.78        21.11 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8289 
       28.73        18.71        11.44         0.69        12.26         2.66 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 
        2.20         7.40         0.26         0.95         3.32         0.26 
TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 
       25.18        15.81        15.68         8.22        12.56         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PF 
       22.26         1.48         0.72         0.53         0.66         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 
        2.83         3.25         0.30         0.07         0.16         0.10 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4444 TCGA-CG-4455 
        0.13         9.34        12.43         3.02        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5727 
       21.99        12.00        22.98         0.99        15.02        79.07 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 
       69.04        12.66        19.13        20.55        18.54        17.19 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6F2 TCGA-D7-A747 
       10.26        12.79        19.50         5.92        15.65         8.38 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF 
        7.40         0.62        11.38        14.07        22.29         5.52 
TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD 
        0.23         1.51        14.17        12.10        24.30        22.75 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD 
        8.98         6.51         6.25        10.19        23.84        27.42 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
        3.45         3.39         5.36        13.08         1.41         6.44 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BW TCGA-RD-A7C1 
        7.82        60.56        61.25         6.08         5.13        16.67 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48        35.24         7.73        22.19        12.79         2.70 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 
       13.35        14.33        11.93        20.81         9.50         9.04 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA6K 
        4.54         5.72        12.43 

$`AMP PEAK 27(12Q15) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94         4.21         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86        14.50        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
       30.25         0.30         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40         3.95         3.02        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         7.76        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       83.24         5.92        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.23        12.03        13.18        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        14.70         7.04        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        18.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43        18.31         8.12        30.71        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 
        9.17        15.91         3.42         2.66        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56        11.01         9.44         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        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       17.29        13.68        19.33        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       15.42        28.01        18.15        15.32        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 
        9.07        12.76        17.49        14.43         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 
        8.05         0.56        12.95        16.31        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
       19.50        13.08        22.19        17.52        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 
       14.04        11.80        19.17        14.79        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
        5.39         9.21        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       16.44         9.86        10.68        13.87         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 
       13.51        12.89         8.98        14.17        12.82        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        5.13        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.07         0.10         0.13         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        3.42        11.31        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       11.93        18.84        18.61        17.85        13.35        15.22 
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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       11.31        11.44         9.76         2.96         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        7.99        16.24        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        17.06        59.54         5.03        13.58         0.56 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         5.92        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.88         8.81        21.21        18.81        18.38         5.19 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51         5.56         1.81        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 
        9.86        45.67        18.21         8.52         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       65.16        36.69        11.70        61.22        18.74        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
        1.71        36.16         7.36         9.73        52.24         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       29.98        17.13        54.12        26.04        16.14        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                        0.07                         0.00 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                       79.07                       122.30 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                       11.24                        13.30 
[1] "0.1 - 79.1 (11.2)"  "0.0 - 122.3 (13.3)"
[1] "hr=" "1.4"
D27V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(12Q15) MUTATED         0        3       12        8        22
  AMP PEAK 27(12Q15) WILD-TYPE      11       16       36       24        55
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(12Q15) MUTATED          18         9         27         17
  AMP PEAK 27(12Q15) WILD-TYPE        66        20         70         55
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(12Q15) MUTATED           14       17         3
  AMP PEAK 27(12Q15) WILD-TYPE         34       34         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  STAGE I                             0                           11
  STAGE IA                            3                           16
  STAGE IB                           12                           36
  STAGE II                            8                           24
  STAGE IIA                          22                           55
  STAGE IIB                          18                           66
  STAGE III                           9                           20
  STAGE IIIA                         27                           70
  STAGE IIIB                         17                           55
  STAGE IIIC                         14                           34
  STAGE IV                           17                           34
  STAGE IVA                           3                            1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 27(12Q15) MUTATED      10  30  80  32
  AMP PEAK 27(12Q15) WILD-TYPE    43  96 200  92
D27V4, multiclass
       clus
vv      AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  T0+T1                         10                           43
  T2                            30                           96
  T3                            80                          200
  T4                            32                           92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 27(12Q15) MUTATED    45  53  29  25
  AMP PEAK 27(12Q15) WILD-TYPE 155 129  67  72
D27V5, multiclass
    clus
vv   AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  N0                         45                          155
  N1                         53                          129
  N2                         29                           67
  N3                         25                           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"
D27V6, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED   125  15
  AMP PEAK 27(12Q15) WILD-TYPE 388  24
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED    125   15
  AMP PEAK 27(12Q15) WILD-TYPE  388   24
   clus
vv  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  0                        125                          388
  1                         15                           24
[1] 2 2
[1] FALSE
D27V7, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED    40 118
  AMP PEAK 27(12Q15) WILD-TYPE 142 309
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED     40  118
  AMP PEAK 27(12Q15) WILD-TYPE  142  309
        clus
vv       AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  FEMALE                         40                          142
  MALE                          118                          309
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 27(12Q15) MUTATED                                      22
  AMP PEAK 27(12Q15) WILD-TYPE                                    49
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(12Q15) MUTATED                                                       38
  AMP PEAK 27(12Q15) WILD-TYPE                                                    124
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(12Q15) MUTATED                                                                  14
  AMP PEAK 27(12Q15) WILD-TYPE                                                                67
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 27(12Q15) MUTATED                                                 26
  AMP PEAK 27(12Q15) WILD-TYPE                                               52
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 27(12Q15) MUTATED                                                          3
  AMP PEAK 27(12Q15) WILD-TYPE                                                       18
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 27(12Q15) MUTATED                                                           2
  AMP PEAK 27(12Q15) WILD-TYPE                                                         6
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 27(12Q15) MUTATED                                          3
  AMP PEAK 27(12Q15) WILD-TYPE                                       10
D27V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 27(12Q15) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    38
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   3
                                                                   clus
vv                                                                  AMP PEAK 27(12Q15) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED     2 156
  AMP PEAK 27(12Q15) WILD-TYPE   4 447
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED      2  156
  AMP PEAK 27(12Q15) WILD-TYPE    4  447
     clus
vv    AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  NO                           2                            4
  YES                        156                          447
[1] 2 2
[1] FALSE
D27V10, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 27(12Q15) MUTATED    86   5   7   4
  AMP PEAK 27(12Q15) WILD-TYPE 261  13  12  21
D27V11, multiclass
    clus
vv   AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  R0                         86                          261
  R1                          5                           13
  R2                          7                           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"
D27V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(12Q15) MUTATED      42                         3
  AMP PEAK 27(12Q15) WILD-TYPE    87                        10
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 27(12Q15) MUTATED                                           0    92
  AMP PEAK 27(12Q15) WILD-TYPE                                         1   293
D27V13, multiclass
                                           clus
vv                                          AMP PEAK 27(12Q15) MUTATED
  ASIAN                                                             42
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             92
                                           clus
vv                                          AMP PEAK 27(12Q15) WILD-TYPE
  ASIAN                                                               87
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED     3 102
  AMP PEAK 27(12Q15) WILD-TYPE   4 292
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED      3  102
  AMP PEAK 27(12Q15) WILD-TYPE    4  292
                        clus
vv                       AMP PEAK 27(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        102
                        clus
vv                       AMP PEAK 27(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          292
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(13Q12.3) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(13Q12.3) MUTATED   125  73
  AMP PEAK 28(13Q12.3) WILD-TYPE 229 148
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           198                            377 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                            73                            148 
$`AMP PEAK 28(13Q12.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92        13.94        32.45 
TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93D 
        7.69         2.63         0.79        14.50        42.77        31.56 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OP 
        3.16        30.25         8.94         4.70        19.99         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
        1.38         4.90         7.13         2.60         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NT TCGA-LN-A5U7 TCGA-LN-A7HW 
       55.50         2.66        12.92        27.12        25.25        12.00 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV 
        7.82        14.70         7.04        53.95        15.78        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29         3.42         9.27        30.71        46.19        10.16 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4279 
       19.73        11.70        11.01         9.44         4.64         9.57 
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
        6.61        15.95        39.12         9.17        32.78        25.61 
TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       21.11         9.21        35.24        18.15        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8362 
       11.44         0.69        12.26         9.60        12.95        13.08 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       14.79        15.85         5.39         9.21        20.22        12.79 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ 
       16.44        15.68         8.22        10.68        13.87        22.26 
TCGA-BR-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-8525 
       20.42         1.15         5.13         3.25        13.15         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
        0.07         0.10         0.13         3.42        12.43         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.20        20.02         3.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5724 
       54.08        47.05         7.07        12.00         1.02        12.03 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       79.07         4.01        69.04         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       19.13        18.54        17.85        17.19        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       10.55        11.31        19.50        17.19        14.66        21.14 
TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       14.27        14.76        11.24         2.96        15.65         8.38 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
        0.62         7.99        72.23         3.48        19.53        17.06 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 
        5.52        12.59        14.17        12.10        12.30        11.84 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
       22.75        25.81         6.51         0.26        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP 
       12.30        27.42         3.45        18.38         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 
       12.59         1.81         5.56        37.64         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
       18.21         8.52         8.61       122.30        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       57.44         8.94        35.61         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       13.25        13.02        21.73        34.45         7.73        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91Q 
        2.70        17.85        23.41        14.33        36.69        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       22.68         1.71        36.16        52.24         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       42.54        11.24        29.98        21.11        12.43         0.79 

$`AMP PEAK 28(13Q12.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RF 
       58.55         7.63         8.94        16.24         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
       23.18        25.22        24.03         6.28         0.30         4.31 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00         3.68        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.32         3.16        58.59        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NI 
        8.71        25.12         7.40         3.95        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        5.92        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         8.02         7.59         5.06        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         1.45        12.69         7.00        20.38 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       42.87        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 
        2.10         2.66        26.70        19.56         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6452 
        6.97         7.43        18.35        30.90         6.18        34.68 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 
       13.87        17.29        13.68        19.33        26.10        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89        12.16         8.98        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       12.82        24.76        23.93        15.42        28.01        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         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-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 
       11.80        19.17         0.26         3.72        25.18         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       11.54        15.81         9.86        12.56         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        1.48        13.41        13.51        12.89         8.98         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-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 
       11.61         0.10        12.62        27.02         1.02         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        29.98        19.07        12.03        21.99         0.00 
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        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       65.10        21.07        11.93        20.55        18.84        18.61 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       13.35        10.26        15.22        12.33        24.72        16.80 
TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 
        7.13        16.24        14.47        21.27        11.38        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX 
       22.29        59.54         5.03        13.58         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       18.08        26.47         1.51         5.92        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         2.10        12.95         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21        18.81         3.39         5.36         5.19        13.08 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74         6.51         5.56         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR 
       60.56        20.15         3.72        19.73        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60         9.24        11.05         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 
      116.38        71.38        16.87        19.04         0.92        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       35.24        27.88        32.48        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.50        12.79         1.87         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        26.24        27.35        64.57        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       11.93        61.22        18.74         7.36         9.50         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        10.62 

  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                         122.3                          122.1 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                         12.79                          12.76 
[1] "0.1 - 122.3 (12.8)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1.1"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(13Q12.3) MUTATED         5        6       12       12        22
  AMP PEAK 28(13Q12.3) WILD-TYPE       6       13       36       20        55
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(13Q12.3) MUTATED          29         6         38         22
  AMP PEAK 28(13Q12.3) WILD-TYPE        55        23         59         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(13Q12.3) MUTATED           16       24         2
  AMP PEAK 28(13Q12.3) WILD-TYPE         32       27         2
D28V3, multiclass
            clus
vv           AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              6                             13
  STAGE IB                             12                             36
  STAGE II                             12                             20
  STAGE IIA                            22                             55
  STAGE IIB                            29                             55
  STAGE III                             6                             23
  STAGE IIIA                           38                             59
  STAGE IIIB                           22                             50
  STAGE IIIC                           16                             32
  STAGE IV                             24                             27
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 28(13Q12.3) MUTATED      20  46  91  43
  AMP PEAK 28(13Q12.3) WILD-TYPE    33  80 189  81
D28V4, multiclass
       clus
vv      AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  T0+T1                           20                             33
  T2                              46                             80
  T3                              91                            189
  T4                              43                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 28(13Q12.3) MUTATED    59  60  37  40
  AMP PEAK 28(13Q12.3) WILD-TYPE 141 122  59  57
D28V5, multiclass
    clus
vv   AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  N0                           59                            141
  N1                           60                            122
  N2                           37                             59
  N3                           40                             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"
D28V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED   174  16
  AMP PEAK 28(13Q12.3) WILD-TYPE 339  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED    174   16
  AMP PEAK 28(13Q12.3) WILD-TYPE  339   23
   clus
vv  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  0                          174                            339
  1                           16                             23
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED    62 149
  AMP PEAK 28(13Q12.3) WILD-TYPE 120 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED     62  149
  AMP PEAK 28(13Q12.3) WILD-TYPE  120  278
        clus
vv       AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  FEMALE                           62                            120
  MALE                            149                            278
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 28(13Q12.3) MUTATED                                      18
  AMP PEAK 28(13Q12.3) WILD-TYPE                                    53
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q12.3) MUTATED                                                       64
  AMP PEAK 28(13Q12.3) WILD-TYPE                                                     98
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(13Q12.3) MUTATED                                                                  34
  AMP PEAK 28(13Q12.3) WILD-TYPE                                                                47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 28(13Q12.3) MUTATED                                                 34
  AMP PEAK 28(13Q12.3) WILD-TYPE                                               44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 28(13Q12.3) MUTATED                                                         10
  AMP PEAK 28(13Q12.3) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 28(13Q12.3) MUTATED                                                           4
  AMP PEAK 28(13Q12.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 28(13Q12.3) MUTATED                                          3
  AMP PEAK 28(13Q12.3) WILD-TYPE                                       10
D28V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 28(13Q12.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      64
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 28(13Q12.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED     3 208
  AMP PEAK 28(13Q12.3) WILD-TYPE   3 395
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED      3  208
  AMP PEAK 28(13Q12.3) WILD-TYPE    3  395
     clus
vv    AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  NO                             3                              3
  YES                          208                            395
[1] 2 2
[1] FALSE
D28V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(13Q12.3) MUTATED   129   9   8   9
  AMP PEAK 28(13Q12.3) WILD-TYPE 218   9  11  16
D28V11, multiclass
    clus
vv   AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  R0                          129                            218
  R1                            9                              9
  R2                            8                             11
  RX                            9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(13Q12.3) MUTATED      36                         8
  AMP PEAK 28(13Q12.3) WILD-TYPE    93                         5
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 28(13Q12.3) MUTATED                                           1
  AMP PEAK 28(13Q12.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 28(13Q12.3) MUTATED     130
  AMP PEAK 28(13Q12.3) WILD-TYPE   255
D28V13, multiclass
                                           clus
vv                                          AMP PEAK 28(13Q12.3) MUTATED
  ASIAN                                                               36
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              130
                                           clus
vv                                          AMP PEAK 28(13Q12.3) WILD-TYPE
  ASIAN                                                                 93
  BLACK OR AFRICAN AMERICAN                                              5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED     2 137
  AMP PEAK 28(13Q12.3) WILD-TYPE   5 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED      2  137
  AMP PEAK 28(13Q12.3) WILD-TYPE    5  257
                        clus
vv                       AMP PEAK 28(13Q12.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          137
                        clus
vv                       AMP PEAK 28(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            257
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(13Q22.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(13Q22.1) MUTATED   146  81
  AMP PEAK 29(13Q22.1) WILD-TYPE 208 140
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           227                            348 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                            81                            140 
$`AMP PEAK 29(13Q22.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       31.27        14.30         5.92        13.94         4.21         7.69 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C 
        0.79        14.50       122.10         3.68        42.77        23.18 
TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       31.56         3.16        30.25         8.94         4.70        19.99 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        7.17         1.38        58.59         7.13         6.94         0.36 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        3.02         2.66        12.92         8.71        13.41        27.12 
TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       46.09        10.45         0.10        15.35         0.10        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59         0.10        12.33        25.25        12.00        12.23 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.82         8.02        14.70         7.04        29.59        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30        15.78        12.69        20.02         5.29         3.42 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-B7-5818 
        9.27        19.96        46.19        10.16        19.73        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-4280 
       11.01         9.44         4.64         7.43         9.57         6.61 
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 
       15.95        39.12         9.17        32.78        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        18.15        28.73         3.45 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8381 
        0.69        12.26         9.60        13.08        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         8.22        10.68        13.87        22.26        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         3.42        12.43         6.58 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
       12.20        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        36.00 
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        69.04         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-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 
       15.65         8.38         0.62         7.99        72.23        19.53 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 
        0.56         5.52        12.59        14.17        12.10        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       11.84        22.75        25.81         6.51         6.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI 
       19.36        23.84        12.30        27.42         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IP-7968 
        5.19         1.41         6.44         6.51         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        37.64         9.86        45.67        18.21         8.52 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       35.24        21.73        34.45        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91K TCGA-VQ-A91Q 
       17.85        23.41        13.35        14.33        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       22.68         1.71        36.16         9.50        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
        4.54        64.18        21.04        42.54        11.24        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        26.04        21.11        12.43 

$`AMP PEAK 29(13Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       25.78        58.55         7.63         8.94        16.24        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
       23.41        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       44.75        60.39        68.02        41.52        25.41        21.70 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       25.22        24.03         6.28         0.30         4.31        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.68        32.61        21.01        47.93        18.35         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        3.16         4.90        29.00         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
       25.12         7.40         3.95        55.50        35.97        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        52.57        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.41        13.15        13.25         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.76        22.39        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        10.52        12.03        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.16         7.59         5.06         6.35         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        7.00        20.38         4.80        15.35         4.44        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI 
       15.91         3.42         2.10         2.66        26.70        19.56 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        9.47         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        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 
       31.20        32.94        12.82        24.76        23.93        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8384 TCGA-BR-8484 
       14.04         3.32        11.80        19.17         3.72        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 
        7.53         0.49        15.81         9.86        12.56         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J4 
        6.08         1.48        13.41        13.51         8.98         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         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 
       11.61         0.10        12.62         3.02        27.02         8.05 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        47.05        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       18.97        22.98        30.97         6.97         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
        0.99        12.03        28.96        79.07        65.10        21.07 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 
       20.55        18.84        18.61        13.35        15.22        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EX 
       16.44         5.92        15.16        13.78        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO 
       11.44         9.76         4.34         7.40         7.13        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-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-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.81         5.36        13.08         6.74        12.59         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        7.82        13.51        60.56        20.15         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       61.25         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
       16.67        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
        0.92        18.48        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        46.26        16.31         2.50         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        26.24        27.35        64.57        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       11.70        11.93        18.74         7.36         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA64 
       55.43         6.58         5.72         2.66        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        32.94        54.12        16.14        10.62         0.79 

  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                        12.590                         12.885 
[1] "0.1 - 122.3 (12.6)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(13Q22.1) MUTATED         6        5       16       15        25
  AMP PEAK 29(13Q22.1) WILD-TYPE       5       14       32       17        52
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(13Q22.1) MUTATED          34         9         40         25
  AMP PEAK 29(13Q22.1) WILD-TYPE        50        20         57         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 29(13Q22.1) MUTATED           16       23         2
  AMP PEAK 29(13Q22.1) WILD-TYPE         32       28         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                              5                             14
  STAGE IB                             16                             32
  STAGE II                             15                             17
  STAGE IIA                            25                             52
  STAGE IIB                            34                             50
  STAGE III                             9                             20
  STAGE IIIA                           40                             57
  STAGE IIIB                           25                             47
  STAGE IIIC                           16                             32
  STAGE IV                             23                             28
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 29(13Q22.1) MUTATED      20  52 107  43
  AMP PEAK 29(13Q22.1) WILD-TYPE    33  74 173  81
D29V4, multiclass
       clus
vv      AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  T0+T1                           20                             33
  T2                              52                             74
  T3                             107                            173
  T4                              43                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 29(13Q22.1) MUTATED    67  72  45  36
  AMP PEAK 29(13Q22.1) WILD-TYPE 133 110  51  61
D29V5, multiclass
    clus
vv   AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  N0                           67                            133
  N1                           72                            110
  N2                           45                             51
  N3                           36                             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"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED   199  15
  AMP PEAK 29(13Q22.1) WILD-TYPE 314  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED    199   15
  AMP PEAK 29(13Q22.1) WILD-TYPE  314   24
   clus
vv  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  0                          199                            314
  1                           15                             24
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED    61 177
  AMP PEAK 29(13Q22.1) WILD-TYPE 121 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED     61  177
  AMP PEAK 29(13Q22.1) WILD-TYPE  121  250
        clus
vv       AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  FEMALE                           61                            121
  MALE                            177                            250
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 29(13Q22.1) MUTATED                                      16
  AMP PEAK 29(13Q22.1) WILD-TYPE                                    55
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(13Q22.1) MUTATED                                                       68
  AMP PEAK 29(13Q22.1) WILD-TYPE                                                     94
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(13Q22.1) MUTATED                                                                  38
  AMP PEAK 29(13Q22.1) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 29(13Q22.1) MUTATED                                                 38
  AMP PEAK 29(13Q22.1) WILD-TYPE                                               40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 29(13Q22.1) MUTATED                                                         10
  AMP PEAK 29(13Q22.1) WILD-TYPE                                                       11
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 29(13Q22.1) MUTATED                                                           5
  AMP PEAK 29(13Q22.1) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 29(13Q22.1) MUTATED                                          3
  AMP PEAK 29(13Q22.1) WILD-TYPE                                       10
D29V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 29(13Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      68
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  AMP PEAK 29(13Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        94
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED     1 237
  AMP PEAK 29(13Q22.1) WILD-TYPE   5 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED      1  237
  AMP PEAK 29(13Q22.1) WILD-TYPE    5  366
     clus
vv    AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  NO                             1                              5
  YES                          237                            366
[1] 2 2
[1] FALSE
D29V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(13Q22.1) MUTATED   137  10   9  10
  AMP PEAK 29(13Q22.1) WILD-TYPE 210   8  10  15
D29V11, multiclass
    clus
vv   AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  R0                          137                            210
  R1                           10                              8
  R2                            9                             10
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(13Q22.1) MUTATED      48                         7
  AMP PEAK 29(13Q22.1) WILD-TYPE    81                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(13Q22.1) MUTATED                                           1
  AMP PEAK 29(13Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 29(13Q22.1) MUTATED     144
  AMP PEAK 29(13Q22.1) WILD-TYPE   241
D29V13, multiclass
                                           clus
vv                                          AMP PEAK 29(13Q22.1) MUTATED
  ASIAN                                                               48
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              144
                                           clus
vv                                          AMP PEAK 29(13Q22.1) WILD-TYPE
  ASIAN                                                                 81
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED     4 149
  AMP PEAK 29(13Q22.1) WILD-TYPE   3 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED      4  149
  AMP PEAK 29(13Q22.1) WILD-TYPE    3  245
                        clus
vv                       AMP PEAK 29(13Q22.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       AMP PEAK 29(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(14Q13.3) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(14Q13.3) MUTATED    53  47
  AMP PEAK 30(14Q13.3) WILD-TYPE 301 174
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           100                            475 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                            47                            174 
$`AMP PEAK 30(14Q13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
       25.78         5.92        32.45         0.85        20.78        18.64 
TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C 
        0.53         9.96        12.16        42.77        23.18         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NG TCGA-L5-A8NN 
       30.25         4.31         3.16         7.43        35.97         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S 
       21.37        13.41         5.92        10.45        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 
       15.35         0.10        12.59        12.59        22.39        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22        12.33        12.23        12.03        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASX 
        8.02        29.59        53.95        20.02        20.38         4.44 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B 
       12.43         8.12        28.11        18.18        46.19        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4187 
        9.17        15.91         3.42         2.10        19.73         4.64 
TCGA-BR-6705 TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-A4J8 
       25.61        18.15        11.44         2.20        20.22        13.51 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4444 
       20.42         1.15        13.64        12.43         7.99        47.05 
TCGA-CG-4460 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6818 TCGA-D7-A6F2 
       21.99        69.04        11.93        19.13        10.55        15.65 
TCGA-EQ-5647 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GC TCGA-IN-8462 TCGA-IN-A6RI 
        0.62         5.92        14.17         3.25        18.81        18.38 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.41         6.74         6.51         5.56        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK 
        8.52        11.05        35.61        18.48        22.19        17.85 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A94R 
       14.33        18.74         1.71        36.16         4.54        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       40.08        17.13        16.14         0.79 

$`AMP PEAK 30(14Q13.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21         7.69         6.21        33.27        20.09 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       23.41        12.82        14.86         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       44.75        60.39        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       21.70        31.56        25.22        24.03         6.28         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        8.94        24.00         3.68         4.70        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        12.92        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         7.76         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W 
       46.09        10.36        12.66        12.43         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 
        0.10        12.46        12.49        12.76         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-M9-A5M8 
       12.33         4.47        25.25        10.52        12.00        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42         4.80        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       18.81        19.96        22.82         1.55        18.31        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 
       42.87        15.06        10.16         2.66        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31        15.58         7.40         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.65        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-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         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        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        12.36        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 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-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         7.99        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39         5.36         5.19        13.08         6.44        12.59 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI 
       20.15        37.64         3.72        19.73         9.86        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       46.26        16.31         2.50        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        22.68         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        11.24        22.09        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        29.98        54.12        26.04        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                         69.04                         122.30 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                         13.20                          12.69 
[1] "0.1 - 69.0 (13.2)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.3"
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(14Q13.3) MUTATED         2        3        5        1        19
  AMP PEAK 30(14Q13.3) WILD-TYPE       9       16       43       31        58
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(14Q13.3) MUTATED          12         8         20         10
  AMP PEAK 30(14Q13.3) WILD-TYPE        72        21         77         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 30(14Q13.3) MUTATED            7       10         1
  AMP PEAK 30(14Q13.3) WILD-TYPE         41       41         3
D30V3, multiclass
            clus
vv           AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  STAGE I                               2                              9
  STAGE IA                              3                             16
  STAGE IB                              5                             43
  STAGE II                              1                             31
  STAGE IIA                            19                             58
  STAGE IIB                            12                             72
  STAGE III                             8                             21
  STAGE IIIA                           20                             77
  STAGE IIIB                           10                             62
  STAGE IIIC                            7                             41
  STAGE IV                             10                             41
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 30(14Q13.3) MUTATED       7  27  47  18
  AMP PEAK 30(14Q13.3) WILD-TYPE    46  99 233 106
D30V4, multiclass
       clus
vv      AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  T0+T1                            7                             46
  T2                              27                             99
  T3                              47                            233
  T4                              18                            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 30(14Q13.3) MUTATED    35  31  14  19
  AMP PEAK 30(14Q13.3) WILD-TYPE 165 151  82  78
D30V5, multiclass
    clus
vv   AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  N0                           35                            165
  N1                           31                            151
  N2                           14                             82
  N3                           19                             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"
D30V6, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED    88   7
  AMP PEAK 30(14Q13.3) WILD-TYPE 425  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED     88    7
  AMP PEAK 30(14Q13.3) WILD-TYPE  425   32
   clus
vv  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  0                           88                            425
  1                            7                             32
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED    21  85
  AMP PEAK 30(14Q13.3) WILD-TYPE 161 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED     21   85
  AMP PEAK 30(14Q13.3) WILD-TYPE  161  342
        clus
vv       AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  FEMALE                           21                            161
  MALE                             85                            342
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 30(14Q13.3) MUTATED                                       6
  AMP PEAK 30(14Q13.3) WILD-TYPE                                    65
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(14Q13.3) MUTATED                                                       22
  AMP PEAK 30(14Q13.3) WILD-TYPE                                                    140
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(14Q13.3) MUTATED                                                                   8
  AMP PEAK 30(14Q13.3) WILD-TYPE                                                                73
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 30(14Q13.3) MUTATED                                                 15
  AMP PEAK 30(14Q13.3) WILD-TYPE                                               63
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 30(14Q13.3) MUTATED                                                          1
  AMP PEAK 30(14Q13.3) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 30(14Q13.3) MUTATED                                                           0
  AMP PEAK 30(14Q13.3) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 30(14Q13.3) MUTATED                                          0
  AMP PEAK 30(14Q13.3) WILD-TYPE                                       13
D30V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 30(14Q13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     0
                                                                   clus
vv                                                                  AMP PEAK 30(14Q13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             73
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED     1 105
  AMP PEAK 30(14Q13.3) WILD-TYPE   5 498
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED      1  105
  AMP PEAK 30(14Q13.3) WILD-TYPE    5  498
     clus
vv    AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  NO                             1                              5
  YES                          105                            498
[1] 2 2
[1] FALSE
D30V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(14Q13.3) MUTATED    40   2   3   3
  AMP PEAK 30(14Q13.3) WILD-TYPE 307  16  16  22
D30V11, multiclass
    clus
vv   AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  R0                           40                            307
  R1                            2                             16
  R2                            3                             16
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(14Q13.3) MUTATED      28                         2
  AMP PEAK 30(14Q13.3) WILD-TYPE   101                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 30(14Q13.3) MUTATED                                           0
  AMP PEAK 30(14Q13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 30(14Q13.3) MUTATED      63
  AMP PEAK 30(14Q13.3) WILD-TYPE   322
D30V13, multiclass
                                           clus
vv                                          AMP PEAK 30(14Q13.3) MUTATED
  ASIAN                                                               28
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               63
                                           clus
vv                                          AMP PEAK 30(14Q13.3) WILD-TYPE
  ASIAN                                                                101
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED     1  67
  AMP PEAK 30(14Q13.3) WILD-TYPE   6 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED      1   67
  AMP PEAK 30(14Q13.3) WILD-TYPE    6  327
                        clus
vv                       AMP PEAK 30(14Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 30(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            327
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(15Q26.1) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(15Q26.1) MUTATED    88  66
  AMP PEAK 31(15Q26.1) WILD-TYPE 266 155
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           154                            421 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                            66                            155 
$`AMP PEAK 31(15Q26.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A50L TCGA-JY-A6F8 
       58.55         7.63         8.94        32.45         0.53       122.10 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ 
       60.39         3.68         3.16        47.93         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NQ 
        2.60         0.36         3.95        55.50        16.47        21.37 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 
       13.41        46.09        10.36        10.45         0.10        22.39 
TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.22        10.52        12.00        12.23        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        14.70         7.04         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
       15.78        20.38        19.96        22.82         1.55        18.31 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-ZR-A9CJ TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 
       11.24         9.17        19.73         6.61        18.35         6.18 
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 
       19.33        12.16         9.21        15.42        18.15        18.71 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8683 TCGA-BR-8687 
       11.44         0.69        19.50        22.19         9.86         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        7.53        22.26         0.53         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 
       13.15         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-4477 
        3.42         6.58        47.05        19.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 
        6.97         1.02        12.03        79.07         4.01        69.04 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       11.93        20.55        18.84        13.35        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6F2 
       10.55        12.33        18.21        14.27        13.78        15.65 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 
        0.62        72.23        11.38        19.53        17.06        13.58 
TCGA-FP-8631 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GY TCGA-HU-A4H5 
        0.56        11.84        25.81        11.77         0.26        12.30 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN 
       27.42         3.45        18.81         3.39        18.38        13.08 
TCGA-IN-A6RO TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.41         5.56        60.56        37.64        45.67        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N6 TCGA-VQ-A8DL 
        6.08         9.24         8.61       122.30         8.94         0.92 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.02        18.48        32.48         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91K TCGA-VQ-A91Q 
       12.79         2.70        17.85        27.35        61.22        20.81 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
        9.50         9.04         4.54        64.18        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        29.98        17.13        54.12 

$`AMP PEAK 31(15Q26.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21         7.69         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        4.67        14.50        12.16        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       18.35         3.32         7.43         8.71        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        3.02         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       52.57         5.92        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33         4.47        12.33        25.25        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W8 
        0.13         5.16         8.02         5.06        29.59         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER 
        4.80        15.35         9.27         4.44        18.81        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       15.06        15.91        10.16         3.42         2.10         2.66 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       24.76        35.24        23.93        28.01        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        17.49        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56        13.87         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
       13.51        12.89         8.98         0.72        14.17        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.07         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.10         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        7.07        12.00        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        15.02        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        19.13        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.19        10.26        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        15.16        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         7.99        16.24        14.47        21.27         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ 
        5.59        12.30        24.20         3.25        22.75        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
        8.81        21.21         5.36         5.19         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
        2.53        20.15         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       61.25         4.60        11.05         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87        19.04         5.79        48.79         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        21.73        34.45        27.88        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        11.93        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.73        52.24         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 
        5.72        21.04         2.66        42.54        22.09        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                        122.30                         116.38 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                        12.905                         12.760 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1"  
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(15Q26.1) MUTATED         5        6       11        9        21
  AMP PEAK 31(15Q26.1) WILD-TYPE       6       13       37       23        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(15Q26.1) MUTATED          15         9         29         17
  AMP PEAK 31(15Q26.1) WILD-TYPE        69        20         68         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 31(15Q26.1) MUTATED            9       18         1
  AMP PEAK 31(15Q26.1) WILD-TYPE         39       33         3
D31V3, multiclass
            clus
vv           AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              6                             13
  STAGE IB                             11                             37
  STAGE II                              9                             23
  STAGE IIA                            21                             56
  STAGE IIB                            15                             69
  STAGE III                             9                             20
  STAGE IIIA                           29                             68
  STAGE IIIB                           17                             55
  STAGE IIIC                            9                             39
  STAGE IV                             18                             33
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 31(15Q26.1) MUTATED      14  40  74  25
  AMP PEAK 31(15Q26.1) WILD-TYPE    39  86 206  99
D31V4, multiclass
       clus
vv      AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  T0+T1                           14                             39
  T2                              40                             86
  T3                              74                            206
  T4                              25                             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 31(15Q26.1) MUTATED    50  48  32  22
  AMP PEAK 31(15Q26.1) WILD-TYPE 150 134  64  75
D31V5, multiclass
    clus
vv   AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  N0                           50                            150
  N1                           48                            134
  N2                           32                             64
  N3                           22                             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"
D31V6, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED   126  14
  AMP PEAK 31(15Q26.1) WILD-TYPE 387  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED    126   14
  AMP PEAK 31(15Q26.1) WILD-TYPE  387   25
   clus
vv  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  0                          126                            387
  1                           14                             25
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED    40 122
  AMP PEAK 31(15Q26.1) WILD-TYPE 142 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED     40  122
  AMP PEAK 31(15Q26.1) WILD-TYPE  142  305
        clus
vv       AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  FEMALE                           40                            142
  MALE                            122                            305
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 31(15Q26.1) MUTATED                                      14
  AMP PEAK 31(15Q26.1) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(15Q26.1) MUTATED                                                       33
  AMP PEAK 31(15Q26.1) WILD-TYPE                                                    129
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 31(15Q26.1) MUTATED                                                                  24
  AMP PEAK 31(15Q26.1) WILD-TYPE                                                                57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 31(15Q26.1) MUTATED                                                 28
  AMP PEAK 31(15Q26.1) WILD-TYPE                                               50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 31(15Q26.1) MUTATED                                                          7
  AMP PEAK 31(15Q26.1) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 31(15Q26.1) MUTATED                                                           2
  AMP PEAK 31(15Q26.1) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 31(15Q26.1) MUTATED                                          2
  AMP PEAK 31(15Q26.1) WILD-TYPE                                       11
D31V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 31(15Q26.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 31(15Q26.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED     2 160
  AMP PEAK 31(15Q26.1) WILD-TYPE   4 443
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED      2  160
  AMP PEAK 31(15Q26.1) WILD-TYPE    4  443
     clus
vv    AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  NO                             2                              4
  YES                          160                            443
[1] 2 2
[1] FALSE
D31V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 31(15Q26.1) MUTATED    83   6   8   5
  AMP PEAK 31(15Q26.1) WILD-TYPE 264  12  11  20
D31V11, multiclass
    clus
vv   AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  R0                           83                            264
  R1                            6                             12
  R2                            8                             11
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(15Q26.1) MUTATED      30                         5
  AMP PEAK 31(15Q26.1) WILD-TYPE    99                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 31(15Q26.1) MUTATED                                           1
  AMP PEAK 31(15Q26.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 31(15Q26.1) MUTATED      99
  AMP PEAK 31(15Q26.1) WILD-TYPE   286
D31V13, multiclass
                                           clus
vv                                          AMP PEAK 31(15Q26.1) MUTATED
  ASIAN                                                               30
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               99
                                           clus
vv                                          AMP PEAK 31(15Q26.1) WILD-TYPE
  ASIAN                                                                 99
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED     2  89
  AMP PEAK 31(15Q26.1) WILD-TYPE   5 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED      2   89
  AMP PEAK 31(15Q26.1) WILD-TYPE    5  305
                        clus
vv                       AMP PEAK 31(15Q26.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           89
                        clus
vv                       AMP PEAK 31(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            305
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(17Q12) MUTATION ANALYSIS
D32V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 32(17Q12) MUTATED   124  85
  AMP PEAK 32(17Q12) WILD-TYPE 230 136
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         209                          366 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                          85                          136 
$`AMP PEAK 32(17Q12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE 
       25.78        14.30        58.55        13.94         8.94         7.69 
TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A938 
       20.09         0.53        17.03        12.82        60.39        25.41 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       23.18        31.56        25.22        30.25         0.30        24.00 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        7.13         2.60         7.40        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NT TCGA-LN-A49L 
       16.47        13.22         5.49         8.71        27.12        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.15        15.35         0.10        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.59        15.52        13.18        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.59         5.06         7.04        29.59        53.95        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        1.45        12.69        20.38         3.42         4.80        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
        9.27         4.44        12.43         1.55        18.31        28.11 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-B7-5818 
       46.19        11.24        15.91        10.16         2.10        11.70 
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8059 
        9.17         9.21        15.42        18.15        18.71        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8369 
       11.44         0.69        12.95         2.66        15.58        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8682 TCGA-BR-8686 
       14.79         5.39        20.22         9.34        16.44        15.68 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68        13.87        22.26         1.48        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 
        0.53        20.42        13.64         3.25        13.15         0.07 
TCGA-CD-8529 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 
        0.13         3.42        11.31        20.02         3.02         7.99 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 
        4.01        47.05        19.07        12.03        21.99        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5730 
       22.98        30.97         1.02         0.99        12.03         4.01 
TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       69.04        18.54        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8579 
       12.79        11.31        12.33        19.50        14.66        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       14.27        16.44        15.16        11.24        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       15.65         4.34         0.62         7.99        16.24        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 
        3.48        14.07         0.56         0.23        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        12.59        12.10        12.30        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI 
       11.77         2.10        12.95        27.42        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        5.56         1.81         7.82         2.53        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
        9.24         8.61         8.94         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.02        18.48        34.45         7.73        46.26        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PT TCGA-VQ-A8PZ 
       12.79         2.70        17.85         1.87        26.24        65.16 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
       20.81        22.68        36.16         9.50         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B 
        4.54        64.18        21.04        42.54        40.08        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        54.12        26.04        21.11         0.79 

$`AMP PEAK 32(17Q12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       31.27         7.63         5.92        16.24         4.21        32.45 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        33.27         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       18.64         3.88         9.30         0.79        23.41         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        42.77        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        6.28         3.16         4.31         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        47.93         7.17         3.16 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
        7.43         6.94         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50         2.66        13.55         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.41        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.03         0.13         5.16        14.70         6.35         9.30 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-VR-A8EO TCGA-VR-A8EP 
        2.89         7.00        20.02         5.29        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
       22.82         8.12        30.71        18.18        42.87        15.06 
TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
        9.17         3.42         2.66        19.73        26.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       12.82        24.76        35.24        23.93        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         9.60        20.55         8.05         0.56        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       11.80        19.17         0.26        15.85         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
        9.21         1.12        12.79        15.81        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 
        7.53         0.49        11.54        15.81         9.86         8.22 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56         7.53         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
       20.65         1.15        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-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-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        9.34        12.43        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       12.62        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       14.01        29.98         0.00         9.01         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
        6.97        36.00         0.99         6.02       105.07        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-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       17.85        15.22        10.55        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       18.21        21.14         5.92        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       11.31         9.76         8.38         7.40         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27        11.38        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8249 
        5.03        13.58         5.52        18.08        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        10.62         0.76        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.25        10.19         0.26        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        3.39         5.36         6.51        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        8.52        61.25         4.60        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44        35.61        16.87        19.04         5.79        48.79 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       35.24        21.73        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       16.31         2.50         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22        18.74         1.71         7.36         9.73        52.24 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U 
       55.43         6.58         5.72         2.66        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       18.41        28.41        32.94        16.14        12.43        10.62 

  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                        0.07                         0.00 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                      12.890                       12.605 
[1] "0.1 - 72.2 (12.9)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.2"
D32V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(17Q12) MUTATED         4        7       16        8        23
  AMP PEAK 32(17Q12) WILD-TYPE       7       12       32       24        54
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(17Q12) MUTATED          24        18         33         25
  AMP PEAK 32(17Q12) WILD-TYPE        60        11         64         47
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 32(17Q12) MUTATED           15       26         2
  AMP PEAK 32(17Q12) WILD-TYPE         33       25         2
D32V3, multiclass
            clus
vv           AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  STAGE I                             4                            7
  STAGE IA                            7                           12
  STAGE IB                           16                           32
  STAGE II                            8                           24
  STAGE IIA                          23                           54
  STAGE IIB                          24                           60
  STAGE III                          18                           11
  STAGE IIIA                         33                           64
  STAGE IIIB                         25                           47
  STAGE IIIC                         15                           33
  STAGE IV                           26                           25
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 32(17Q12) MUTATED      23  42  96  42
  AMP PEAK 32(17Q12) WILD-TYPE    30  84 184  82
D32V4, multiclass
       clus
vv      AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  T0+T1                         23                           30
  T2                            42                           84
  T3                            96                          184
  T4                            42                           82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 32(17Q12) MUTATED    64  65  36  36
  AMP PEAK 32(17Q12) WILD-TYPE 136 117  60  61
D32V5, multiclass
    clus
vv   AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  N0                         64                          136
  N1                         65                          117
  N2                         36                           60
  N3                         36                           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"
D32V6, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED   166  21
  AMP PEAK 32(17Q12) WILD-TYPE 347  18
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED    166   21
  AMP PEAK 32(17Q12) WILD-TYPE  347   18
   clus
vv  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  0                        166                          347
  1                         21                           18
[1] 2 2
[1] FALSE
D32V7, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED    49 167
  AMP PEAK 32(17Q12) WILD-TYPE 133 260
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED     49  167
  AMP PEAK 32(17Q12) WILD-TYPE  133  260
        clus
vv       AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  FEMALE                         49                          133
  MALE                          167                          260
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 32(17Q12) MUTATED                                       9
  AMP PEAK 32(17Q12) WILD-TYPE                                    62
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(17Q12) MUTATED                                                       46
  AMP PEAK 32(17Q12) WILD-TYPE                                                    116
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 32(17Q12) MUTATED                                                                  35
  AMP PEAK 32(17Q12) WILD-TYPE                                                                46
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 32(17Q12) MUTATED                                                 38
  AMP PEAK 32(17Q12) WILD-TYPE                                               40
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 32(17Q12) MUTATED                                                          6
  AMP PEAK 32(17Q12) WILD-TYPE                                                       15
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 32(17Q12) MUTATED                                                           4
  AMP PEAK 32(17Q12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 32(17Q12) MUTATED                                          6
  AMP PEAK 32(17Q12) WILD-TYPE                                        7
D32V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 32(17Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   6
                                                                   clus
vv                                                                  AMP PEAK 32(17Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED     2 214
  AMP PEAK 32(17Q12) WILD-TYPE   4 389
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED      2  214
  AMP PEAK 32(17Q12) WILD-TYPE    4  389
     clus
vv    AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  NO                           2                            4
  YES                        214                          389
[1] 2 2
[1] FALSE
D32V10, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 32(17Q12) MUTATED   121   1  12   3
  AMP PEAK 32(17Q12) WILD-TYPE 226  17   7  22
D32V11, multiclass
    clus
vv   AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  R0                        121                          226
  R1                          1                           17
  R2                         12                            7
  RX                          3                           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(17Q12) MUTATED      38                        10
  AMP PEAK 32(17Q12) WILD-TYPE    91                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 32(17Q12) MUTATED                                           1   134
  AMP PEAK 32(17Q12) WILD-TYPE                                         0   251
D32V13, multiclass
                                           clus
vv                                          AMP PEAK 32(17Q12) MUTATED
  ASIAN                                                             38
  BLACK OR AFRICAN AMERICAN                                         10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            134
                                           clus
vv                                          AMP PEAK 32(17Q12) WILD-TYPE
  ASIAN                                                               91
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED     1 128
  AMP PEAK 32(17Q12) WILD-TYPE   6 266
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED      1  128
  AMP PEAK 32(17Q12) WILD-TYPE    6  266
                        clus
vv                       AMP PEAK 32(17Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                        128
                        clus
vv                       AMP PEAK 32(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          266
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(18P11.32) MUTATION ANALYSIS
D33V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 33(18P11.32) MUTATED    97  63
  AMP PEAK 33(18P11.32) WILD-TYPE 257 158
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            160                             415 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                             63                             158 
$`AMP PEAK 33(18P11.32) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A50L 
        7.63        13.94        16.24         4.21        32.45         0.53 
TCGA-IG-A625 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       12.82        14.50        12.16        44.75        60.39         3.68 
TCGA-JY-A938 TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OM TCGA-L5-A4OO 
       25.41         3.16         4.31         8.94        47.93         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y 
        1.38         3.16         4.90         7.13         2.60         0.36 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        13.48        16.47        13.22         5.49        21.37 
TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       27.12        46.09        10.36        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        13.25         0.10        12.46        12.76        12.59 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        13.22         4.47        25.25        12.03        13.18 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        5.06        53.95        12.69        20.38         3.42         4.80 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       28.11        18.18        42.87        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6565 
        2.10         2.66         9.44         6.97        18.35         9.17 
TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
        9.21        28.01        15.32         3.45        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        9.60         8.05         2.20        15.58         7.40        13.08 
TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8677 TCGA-BR-8687 
        3.32         9.21        20.22         1.12         0.49         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       13.87        22.26        12.89         0.72        13.51        20.65 
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         3.42 
TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6518 
        9.34        12.20        21.99        22.98        12.03        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.84        18.54        17.19        10.26        15.22        12.79 
TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A 
       14.66        13.78        11.31         2.96        15.65         7.40 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 
       11.38        19.53         0.56         5.52         0.23        26.47 
TCGA-HU-8243 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU 
        5.92        10.62         0.76        22.75        25.81         6.25 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       23.84        27.42        18.38        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.74         5.56         7.82        60.56        45.67        18.21 
TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8E3 
       61.25         8.61       115.69        35.61         0.92        21.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E 
       22.19         2.70        17.85         1.87         9.27        11.93 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94P 
       18.74         1.71         9.50         9.04        64.18         2.66 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       22.09        40.08        32.94         0.79 

$`AMP PEAK 33(18P11.32) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55         5.92         8.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
        0.79        23.41         9.96        14.86         4.67       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        42.77        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE 
       25.22        24.03         6.28        30.25         0.30        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.68         4.70        32.61        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        7.17        58.59        29.00         7.43         6.94         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
       25.12         7.40         3.95         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       12.92        13.55         7.76         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       52.57         5.92        10.45        12.66        12.43         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        22.39         0.10        15.52        11.54 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        10.52        12.00        12.23         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02         5.29        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
        8.12        30.71        46.19        15.06        15.91        10.16 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.61         4.64         7.43        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82        24.76        35.24        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       17.49        14.43        12.26        20.55         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.66        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 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.18        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36         0.46        20.42         1.15        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-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6522 
        7.99        12.36        12.66        11.93        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        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-A747 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         3.48        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.03        13.58        18.08         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       14.17        11.41        12.10        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51         1.81        13.51         2.53         5.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       20.15        37.64         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24        11.05         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        16.87        19.04         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        35.24        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       32.48         7.73        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50        12.79        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       61.22        20.81        22.68        36.16         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       21.04        42.54        11.24        18.41        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                         115.69                          122.30 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                          12.03                           13.02 
[1] "0.1 - 115.7 (12.0)" "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D33V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 33(18P11.32) MUTATED         2        6       10        6        22
  AMP PEAK 33(18P11.32) WILD-TYPE       9       13       38       26        55
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(18P11.32) MUTATED          25        13         23         14
  AMP PEAK 33(18P11.32) WILD-TYPE        59        16         74         58
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 33(18P11.32) MUTATED           19       16         3
  AMP PEAK 33(18P11.32) WILD-TYPE         29       35         1
D33V3, multiclass
            clus
vv           AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  STAGE I                                2                               9
  STAGE IA                               6                              13
  STAGE IB                              10                              38
  STAGE II                               6                              26
  STAGE IIA                             22                              55
  STAGE IIB                             25                              59
  STAGE III                             13                              16
  STAGE IIIA                            23                              74
  STAGE IIIB                            14                              58
  STAGE IIIC                            19                              29
  STAGE IV                              16                              35
  STAGE IVA                              3                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 33(18P11.32) MUTATED      16  27  84  34
  AMP PEAK 33(18P11.32) WILD-TYPE    37  99 196  90
D33V4, multiclass
       clus
vv      AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  T0+T1                            16                              37
  T2                               27                              99
  T3                               84                             196
  T4                               34                              90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 33(18P11.32) MUTATED    54  52  21  33
  AMP PEAK 33(18P11.32) WILD-TYPE 146 130  75  64
D33V5, multiclass
    clus
vv   AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  N0                            54                             146
  N1                            52                             130
  N2                            21                              75
  N3                            33                              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"
D33V6, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED   137  13
  AMP PEAK 33(18P11.32) WILD-TYPE 376  26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED    137   13
  AMP PEAK 33(18P11.32) WILD-TYPE  376   26
   clus
vv  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  0                           137                             376
  1                            13                              26
[1] 2 2
[1] FALSE
D33V7, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED    45 126
  AMP PEAK 33(18P11.32) WILD-TYPE 137 301
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED     45  126
  AMP PEAK 33(18P11.32) WILD-TYPE  137  301
        clus
vv       AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  FEMALE                            45                             137
  MALE                             126                             301
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 33(18P11.32) MUTATED                                      13
  AMP PEAK 33(18P11.32) WILD-TYPE                                    58
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(18P11.32) MUTATED                                                       39
  AMP PEAK 33(18P11.32) WILD-TYPE                                                    123
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 33(18P11.32) MUTATED                                                                  16
  AMP PEAK 33(18P11.32) WILD-TYPE                                                                65
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 33(18P11.32) MUTATED                                                 24
  AMP PEAK 33(18P11.32) WILD-TYPE                                               54
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 33(18P11.32) MUTATED                                                          5
  AMP PEAK 33(18P11.32) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 33(18P11.32) MUTATED                                                           2
  AMP PEAK 33(18P11.32) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 33(18P11.32) MUTATED                                          7
  AMP PEAK 33(18P11.32) WILD-TYPE                                        6
D33V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 33(18P11.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      7
                                                                   clus
vv                                                                  AMP PEAK 33(18P11.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED     3 168
  AMP PEAK 33(18P11.32) WILD-TYPE   3 435
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED      3  168
  AMP PEAK 33(18P11.32) WILD-TYPE    3  435
     clus
vv    AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  NO                              3                               3
  YES                           168                             435
[1] 2 2
[1] FALSE
D33V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 33(18P11.32) MUTATED    83   5   6   6
  AMP PEAK 33(18P11.32) WILD-TYPE 264  13  13  19
D33V11, multiclass
    clus
vv   AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  R0                            83                             264
  R1                             5                              13
  R2                             6                              13
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(18P11.32) MUTATED      44                         1
  AMP PEAK 33(18P11.32) WILD-TYPE    85                        12
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 33(18P11.32) MUTATED                                           1
  AMP PEAK 33(18P11.32) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 33(18P11.32) MUTATED     105
  AMP PEAK 33(18P11.32) WILD-TYPE   280
D33V13, multiclass
                                           clus
vv                                          AMP PEAK 33(18P11.32) MUTATED
  ASIAN                                                                44
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               105
                                           clus
vv                                          AMP PEAK 33(18P11.32) WILD-TYPE
  ASIAN                                                                  85
  BLACK OR AFRICAN AMERICAN                                              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED     3 109
  AMP PEAK 33(18P11.32) WILD-TYPE   4 285
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED      3  109
  AMP PEAK 33(18P11.32) WILD-TYPE    4  285
                        clus
vv                       AMP PEAK 33(18P11.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           109
                        clus
vv                       AMP PEAK 33(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             285
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 34(18Q11.2) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 34(18Q11.2) MUTATED   107  72
  AMP PEAK 34(18Q11.2) WILD-TYPE 247 149
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           179                            396 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                            72                            149 
$`AMP PEAK 34(18Q11.2) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A50L 
       58.55         7.63        13.94         4.21        33.27         0.53 
TCGA-IG-A625 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M 
       12.82        60.39        42.77         3.16        30.25         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OW 
       24.00         4.70        18.35         3.32         3.16         7.13 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        2.60         0.36         3.02        55.50         2.66        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       13.22         5.49        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       46.09        10.36         5.92         0.10        12.76        12.59 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.33        25.25        13.18         7.82         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RE 
       29.59        53.95        15.78        12.69        20.38         4.80 
TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
       22.82        18.18        42.87        11.24        15.91         2.10 
TCGA-Z6-AAPN TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6564 
        2.66         9.44         6.97         7.43        18.35        26.10 
TCGA-BR-6565 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 
        9.17        15.42        15.32        28.73         3.45         0.69 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        9.60         8.05        12.95         2.20        15.58         7.40 
TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       13.08         3.32        14.79         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 
        1.12        15.81         0.49        11.54        15.68         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
       13.87        22.26        12.89         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8526 
       20.65         1.15         2.83         3.25        13.15         0.07 
TCGA-CD-8529 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        0.13         3.42        12.43        12.20        20.02         3.02 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        19.07        21.99         7.07        12.00 
TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.03        11.93        19.13        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EV 
       10.26        15.22        12.79        14.66        13.78        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       11.31        11.44         2.96         7.40         0.62        72.23 
TCGA-F1-A72C TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 
       11.38         0.56         5.52         0.23        26.47         5.92 
TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H4 TCGA-HU-A4H5 
       12.59         0.76        22.75         8.98        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
        9.67        27.42        18.81        18.38         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F7 
        1.41         6.44         6.74         1.81         7.82        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A805 TCGA-RD-A7BW 
       37.64         9.86        45.67        61.25         9.24         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       16.67       115.69        35.61         5.79         0.92         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PZ 
       13.02        18.48         2.70         1.87         9.27        65.16 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A92D 
       11.93        18.74         1.71        36.16         9.04        64.18 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       42.54        22.09        40.08        32.94         0.79 

$`AMP PEAK 34(18Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69         6.21        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI 
        6.28         0.30         4.31         3.68        32.61        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01        47.93         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43         6.94         8.71        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM 
        3.95        35.97        12.92        16.47        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37         8.71        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
        0.10        13.15        15.35         0.10        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.59        12.49        22.39         0.10        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6L4 
       12.03         0.13        33.11         5.16         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04         6.35         9.30         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.02         5.29         3.42        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       28.11        30.71        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        9.47         6.61         4.64        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       19.33        39.12        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       12.82         9.21        24.76        35.24        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       18.15        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 
       14.43        11.44        12.26        20.55         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       16.31         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 
        0.26        15.85         5.39         9.21        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       13.45         6.28         7.53        15.81        16.44         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       13.51         8.98        14.17         0.53        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 
        0.46        20.42        13.64        11.57         5.13        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        11.31        11.61         6.58         0.10        12.62 
TCGA-CG-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-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        12.03         0.00         9.01        18.97 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 
       12.66        20.55        18.84        18.61        17.85        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-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 
        5.92        15.16        14.76        13.71         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         7.99        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
       59.54         5.03        13.58        18.08         1.51        14.27 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        19.36         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR 
       21.21         3.45         3.39         5.36        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG 
        5.56        13.51         2.53         5.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       19.73        18.21         8.52         6.08         4.60        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DV 
       57.44         8.94        16.87        19.04        48.79        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       12.79        17.85        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       27.35        64.57        14.33        36.69        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        22.68         7.36         9.50         9.73        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        11.24        18.41        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        12.43        10.62 

  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                         12.30                          13.05 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.1"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 34(18Q11.2) MUTATED         6        6       13        8        20
  AMP PEAK 34(18Q11.2) WILD-TYPE       5       13       35       24        57
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 34(18Q11.2) MUTATED          22        11         32         19
  AMP PEAK 34(18Q11.2) WILD-TYPE        62        18         65         53
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 34(18Q11.2) MUTATED           19       19         2
  AMP PEAK 34(18Q11.2) WILD-TYPE         29       32         2
D34V3, multiclass
            clus
vv           AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                              6                             13
  STAGE IB                             13                             35
  STAGE II                              8                             24
  STAGE IIA                            20                             57
  STAGE IIB                            22                             62
  STAGE III                            11                             18
  STAGE IIIA                           32                             65
  STAGE IIIB                           19                             53
  STAGE IIIC                           19                             29
  STAGE IV                             19                             32
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 34(18Q11.2) MUTATED      19  34  84  43
  AMP PEAK 34(18Q11.2) WILD-TYPE    34  92 196  81
D34V4, multiclass
       clus
vv      AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  T0+T1                           19                             34
  T2                              34                             92
  T3                              84                            196
  T4                              43                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 34(18Q11.2) MUTATED    59  55  32  35
  AMP PEAK 34(18Q11.2) WILD-TYPE 141 127  64  62
D34V5, multiclass
    clus
vv   AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  N0                           59                            141
  N1                           55                            127
  N2                           32                             64
  N3                           35                             62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED   157  14
  AMP PEAK 34(18Q11.2) WILD-TYPE 356  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED    157   14
  AMP PEAK 34(18Q11.2) WILD-TYPE  356   25
   clus
vv  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  0                          157                            356
  1                           14                             25
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED    57 135
  AMP PEAK 34(18Q11.2) WILD-TYPE 125 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED     57  135
  AMP PEAK 34(18Q11.2) WILD-TYPE  125  292
        clus
vv       AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  FEMALE                           57                            125
  MALE                            135                            292
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 34(18Q11.2) MUTATED                                      15
  AMP PEAK 34(18Q11.2) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(18Q11.2) MUTATED                                                       57
  AMP PEAK 34(18Q11.2) WILD-TYPE                                                    105
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 34(18Q11.2) MUTATED                                                                  19
  AMP PEAK 34(18Q11.2) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 34(18Q11.2) MUTATED                                                 25
  AMP PEAK 34(18Q11.2) WILD-TYPE                                               53
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 34(18Q11.2) MUTATED                                                          7
  AMP PEAK 34(18Q11.2) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 34(18Q11.2) MUTATED                                                           4
  AMP PEAK 34(18Q11.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 34(18Q11.2) MUTATED                                          8
  AMP PEAK 34(18Q11.2) WILD-TYPE                                        5
D34V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 34(18Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  AMP PEAK 34(18Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED     4 188
  AMP PEAK 34(18Q11.2) WILD-TYPE   2 415
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED      4  188
  AMP PEAK 34(18Q11.2) WILD-TYPE    2  415
     clus
vv    AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          188                            415
[1] 2 2
[1] FALSE
D34V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 34(18Q11.2) MUTATED   104   8   8   8
  AMP PEAK 34(18Q11.2) WILD-TYPE 243  10  11  17
D34V11, multiclass
    clus
vv   AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  R0                          104                            243
  R1                            8                             10
  R2                            8                             11
  RX                            8                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(18Q11.2) MUTATED      36                         3
  AMP PEAK 34(18Q11.2) WILD-TYPE    93                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 34(18Q11.2) MUTATED                                           0
  AMP PEAK 34(18Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 34(18Q11.2) MUTATED     128
  AMP PEAK 34(18Q11.2) WILD-TYPE   257
D34V13, multiclass
                                           clus
vv                                          AMP PEAK 34(18Q11.2) MUTATED
  ASIAN                                                               36
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              128
                                           clus
vv                                          AMP PEAK 34(18Q11.2) WILD-TYPE
  ASIAN                                                                 93
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED     3 122
  AMP PEAK 34(18Q11.2) WILD-TYPE   4 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED      3  122
  AMP PEAK 34(18Q11.2) WILD-TYPE    4  272
                        clus
vv                       AMP PEAK 34(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       AMP PEAK 34(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            272
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(19P13.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(19P13.2) MUTATED    55  17
  AMP PEAK 35(19P13.2) WILD-TYPE 299 204
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                            72                            503 
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                            17                            204 
$`AMP PEAK 35(19P13.2) MUTATED`
TCGA-2H-A9GH TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A51D TCGA-L5-A43C TCGA-L5-A43J 
       31.27        20.09        20.12        17.03         3.16         4.31 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NF 
        3.16        29.00         2.60         0.36         3.95         2.66 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A4A1 
       13.55        27.12         5.92        13.41         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-R6-A8W8 TCGA-S8-A6BW 
       12.76         0.10        25.25        12.00         2.89        20.38 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR 
       15.35         9.27        18.81        28.11        15.91        10.16 
TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6801 TCGA-BR-7959 TCGA-BR-8370 TCGA-BR-A453 
        9.47        17.29        21.11        18.71         3.32         6.08 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8533 
       13.51        20.65        13.64        13.18         0.10         0.13 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-5722 TCGA-CG-5727 TCGA-D7-6518 TCGA-D7-6519 
        3.42         7.99         0.99        79.07        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4YU 
       18.54        13.35        17.19        15.22        15.98        16.44 
TCGA-D7-A6EV TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 
       11.24        16.24        11.38         0.56         5.52        14.17 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-IN-7808 TCGA-IN-A6RP TCGA-IN-A7NT TCGA-RD-A7BT 
       12.10        22.75         3.45         6.44         5.56         8.61 
TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A91S TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6A 
       48.79        21.73        22.68         4.54        64.18        32.94 

$`AMP PEAK 35(19P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       33.27         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       60.39        68.02         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        6.94         8.71        25.12         7.40         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       46.09        10.36        10.45        12.66        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35        13.25         0.10        12.46        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        5.29         3.42         4.80         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD 
       42.87        46.19        15.06        11.24         9.17         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.44         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        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-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        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
       14.04        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        8.22        10.68        12.56        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         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-8535 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97        36.00         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        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        11.93        18.84 
TCGA-D7-6522 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        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        21.14        20.91        14.27         5.92        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-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        0.62         7.99        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-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 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       13.08         1.41         6.74        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        35.24        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       20.81         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                         79.07                         122.30 
  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE 
                         13.38                          12.66 
[1] "0.1 - 79.1 (13.4)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1.6"
D35V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 35(19P13.2) MUTATED         0        1        4        3        14
  AMP PEAK 35(19P13.2) WILD-TYPE      11       18       44       29        63
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 35(19P13.2) MUTATED          11         4         15          8
  AMP PEAK 35(19P13.2) WILD-TYPE        73        25         82         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 35(19P13.2) MUTATED            3        4         2
  AMP PEAK 35(19P13.2) WILD-TYPE         45       47         2
D35V3, multiclass
            clus
vv           AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  STAGE I                               0                             11
  STAGE IA                              1                             18
  STAGE IB                              4                             44
  STAGE II                              3                             29
  STAGE IIA                            14                             63
  STAGE IIB                            11                             73
  STAGE III                             4                             25
  STAGE IIIA                           15                             82
  STAGE IIIB                            8                             64
  STAGE IIIC                            3                             45
  STAGE IV                              4                             47
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 35(19P13.2) MUTATED       8  14  40  11
  AMP PEAK 35(19P13.2) WILD-TYPE    45 112 240 113
D35V4, multiclass
       clus
vv      AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  T0+T1                            8                             45
  T2                              14                            112
  T3                              40                            240
  T4                              11                            113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 35(19P13.2) MUTATED    32  18  11  11
  AMP PEAK 35(19P13.2) WILD-TYPE 168 164  85  86
D35V5, multiclass
    clus
vv   AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  N0                           32                            168
  N1                           18                            164
  N2                           11                             85
  N3                           11                             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                                cls
clus                               0   1
  AMP PEAK 35(19P13.2) MUTATED    58   6
  AMP PEAK 35(19P13.2) WILD-TYPE 455  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(19P13.2) MUTATED     58    6
  AMP PEAK 35(19P13.2) WILD-TYPE  455   33
   clus
vv  AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  0                           58                            455
  1                            6                             33
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                               0   1
  AMP PEAK 35(19P13.2) MUTATED    18  58
  AMP PEAK 35(19P13.2) WILD-TYPE 164 369
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(19P13.2) MUTATED     18   58
  AMP PEAK 35(19P13.2) WILD-TYPE  164  369
        clus
vv       AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  FEMALE                           18                            164
  MALE                             58                            369
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 35(19P13.2) MUTATED                                       8
  AMP PEAK 35(19P13.2) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(19P13.2) MUTATED                                                       16
  AMP PEAK 35(19P13.2) WILD-TYPE                                                    146
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 35(19P13.2) MUTATED                                                                   9
  AMP PEAK 35(19P13.2) WILD-TYPE                                                                72
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 35(19P13.2) MUTATED                                                 10
  AMP PEAK 35(19P13.2) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 35(19P13.2) MUTATED                                                          1
  AMP PEAK 35(19P13.2) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 35(19P13.2) MUTATED                                                           0
  AMP PEAK 35(19P13.2) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 35(19P13.2) MUTATED                                          2
  AMP PEAK 35(19P13.2) WILD-TYPE                                       11
D35V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 35(19P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  AMP PEAK 35(19P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                                cls
clus                               0   1
  AMP PEAK 35(19P13.2) MUTATED     0  76
  AMP PEAK 35(19P13.2) WILD-TYPE   6 527
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(19P13.2) MUTATED      0   76
  AMP PEAK 35(19P13.2) WILD-TYPE    6  527
     clus
vv    AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  NO                             0                              6
  YES                           76                            527
[1] 2 2
[1] FALSE
D35V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(19P13.2) MUTATED    35   2   4   2
  AMP PEAK 35(19P13.2) WILD-TYPE 312  16  15  23
D35V11, multiclass
    clus
vv   AMP PEAK 35(19P13.2) MUTATED AMP PEAK 35(19P13.2) WILD-TYPE
  R0                           35                            312
  R1                            2                             16
  R2                            4                             15
  RX                            2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 35(19P13.2) MUTATED      17                         2
  AMP PEAK 35(19P13.2) WILD-TYPE   112                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 35(19P13.2) MUTATED                                           1
  AMP PEAK 35(19P13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 35(19P13.2) MUTATED      49
  AMP PEAK 35(19P13.2) WILD-TYPE   336
D35V13, multiclass
                                           clus
vv                                          AMP PEAK 35(19P13.2) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               49
                                           clus
vv                                          AMP PEAK 35(19P13.2) WILD-TYPE
  ASIAN                                                                112
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                                cls
clus                               0   1
  AMP PEAK 35(19P13.2) MUTATED     0  52
  AMP PEAK 35(19P13.2) WILD-TYPE   7 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(19P13.2) MUTATED      0   52
  AMP PEAK 35(19P13.2) WILD-TYPE    7  342
                        clus
vv                       AMP PEAK 35(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       AMP PEAK 35(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            342
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 36(19Q12) MUTATION ANALYSIS
D36V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 36(19Q12) MUTATED   107  60
  AMP PEAK 36(19Q12) WILD-TYPE 247 161
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                         167                          408 
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                          60                          161 
$`AMP PEAK 36(19Q12) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3QL 
       31.27        58.55         7.63         8.94         7.69        20.09 
TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OE 
        3.88        23.41        14.50        42.77         3.16        24.00 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.68        32.61        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NK TCGA-L5-A8NN 
       58.59         3.95        55.50        35.97        13.55         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49U TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A7HW 
       10.45        15.35        12.59        22.39         0.10        12.00 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        0.13         5.06        14.70        29.59        53.95        15.78 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7I 
       12.69        20.38        15.35        28.11        42.87        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 
       10.16         2.10         9.47        17.29        19.33         9.21 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 
       15.42        28.01        28.73         3.45        18.71        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 
        0.69        12.95         2.66        16.31         2.20         3.32 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8690 
       14.79         9.21         1.12         9.34        11.54        10.68 
TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 
        6.08         0.72        13.51        20.65        13.64        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 
       13.18         0.30         0.07         0.07         0.07         0.16 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         3.42         9.34        12.43        11.61        12.20 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 
       54.08        47.05        19.07        21.99        22.98         0.99 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        4.01        12.36        11.93        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8578 
       17.19        10.26        15.22        10.55        12.33        21.14 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       16.44        13.78         2.96         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF 
       16.24        72.23         3.48        14.07         0.56         5.52 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD 
       14.27        12.59        14.17        12.10        24.30        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       25.81        11.77         2.10        12.95        12.30        27.42 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F5 
        3.45        18.38         5.19         1.41         6.44         5.56 
TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7BW 
       60.56        45.67        18.21         6.08         8.61         5.13 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 
       35.61         5.79        48.79         5.46        13.25        35.24 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91N 
        7.73        22.19        17.85         1.87        36.69        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
       22.68         1.71        36.16         9.50         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6K 
        4.54        21.04        17.13        54.12        12.43 

$`AMP PEAK 36(19Q12) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       44.75        60.39        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         4.70        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       21.01        47.93         7.17         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.02         2.66        12.92        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M 
       13.22         7.76        21.37        13.41        83.24        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41         0.10        13.15         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A8 
        0.10        12.46        12.59        12.49        12.76        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       10.52        12.23        12.03        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 
        7.82         8.02         7.59         7.04         6.35         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45         7.00        20.02         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN 
       46.19        15.06        11.24         9.17         3.42         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32        12.43         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
       25.18        20.22        12.79        15.81        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        12.56        13.87         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
       12.82         0.66        19.36         0.46        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8527 
       11.57         5.13         2.83         3.25         0.07         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 
       11.31         6.58         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02       105.07        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       79.07        65.10        69.04        21.07         7.99        12.66 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       20.55        18.61        17.85        13.35        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       14.66        20.91        14.27         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.71        11.24        11.31        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        8.38         4.34         7.40        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 
        0.23        18.08        26.47         1.51         5.92        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.25        10.19         0.26        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.88         8.81        21.21        18.81         3.39         5.36 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         6.74        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        7.82        13.51         2.53        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       19.73         9.86         8.52        61.25         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        13.02        18.48        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       11.93        61.22        20.81         7.36         9.73        52.24 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        64.18         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        26.04        16.14        21.11        10.62         0.79 

  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                        0.07                         0.00 
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE 
                       12.59                        12.79 
[1] "0.1 - 72.2 (12.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D36V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 36(19Q12) MUTATED         3        5       13       10        21
  AMP PEAK 36(19Q12) WILD-TYPE       8       14       35       22        56
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 36(19Q12) MUTATED          27         9         35         19
  AMP PEAK 36(19Q12) WILD-TYPE        57        20         62         53
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 36(19Q12) MUTATED           10       14         2
  AMP PEAK 36(19Q12) WILD-TYPE         38       37         2
D36V3, multiclass
            clus
vv           AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  STAGE I                             3                            8
  STAGE IA                            5                           14
  STAGE IB                           13                           35
  STAGE II                           10                           22
  STAGE IIA                          21                           56
  STAGE IIB                          27                           57
  STAGE III                           9                           20
  STAGE IIIA                         35                           62
  STAGE IIIB                         19                           53
  STAGE IIIC                         10                           38
  STAGE IV                           14                           37
  STAGE IVA                           2                            2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 36(19Q12) MUTATED      15  37  93  27
  AMP PEAK 36(19Q12) WILD-TYPE    38  89 187  97
D36V4, multiclass
       clus
vv      AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  T0+T1                         15                           38
  T2                            37                           89
  T3                            93                          187
  T4                            27                           97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 36(19Q12) MUTATED    53  59  25  32
  AMP PEAK 36(19Q12) WILD-TYPE 147 123  71  65
D36V5, multiclass
    clus
vv   AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  N0                         53                          147
  N1                         59                          123
  N2                         25                           71
  N3                         32                           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"
D36V6, binary
                              cls
clus                             0   1
  AMP PEAK 36(19Q12) MUTATED   148  11
  AMP PEAK 36(19Q12) WILD-TYPE 365  28
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(19Q12) MUTATED    148   11
  AMP PEAK 36(19Q12) WILD-TYPE  365   28
   clus
vv  AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  0                        148                          365
  1                         11                           28
[1] 2 2
[1] FALSE
D36V7, binary
                              cls
clus                             0   1
  AMP PEAK 36(19Q12) MUTATED    49 132
  AMP PEAK 36(19Q12) WILD-TYPE 133 295
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(19Q12) MUTATED     49  132
  AMP PEAK 36(19Q12) WILD-TYPE  133  295
        clus
vv       AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  FEMALE                         49                          133
  MALE                          132                          295
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 36(19Q12) MUTATED                                      17
  AMP PEAK 36(19Q12) WILD-TYPE                                    54
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(19Q12) MUTATED                                                       46
  AMP PEAK 36(19Q12) WILD-TYPE                                                    116
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 36(19Q12) MUTATED                                                                  23
  AMP PEAK 36(19Q12) WILD-TYPE                                                                58
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 36(19Q12) MUTATED                                                 27
  AMP PEAK 36(19Q12) WILD-TYPE                                               51
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 36(19Q12) MUTATED                                                          7
  AMP PEAK 36(19Q12) WILD-TYPE                                                       14
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 36(19Q12) MUTATED                                                           4
  AMP PEAK 36(19Q12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 36(19Q12) MUTATED                                          4
  AMP PEAK 36(19Q12) WILD-TYPE                                        9
D36V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 36(19Q12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   4
                                                                   clus
vv                                                                  AMP PEAK 36(19Q12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                              cls
clus                             0   1
  AMP PEAK 36(19Q12) MUTATED     4 177
  AMP PEAK 36(19Q12) WILD-TYPE   2 426
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(19Q12) MUTATED      4  177
  AMP PEAK 36(19Q12) WILD-TYPE    2  426
     clus
vv    AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  NO                           4                            2
  YES                        177                          426
[1] 2 2
[1] FALSE
D36V10, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 36(19Q12) MUTATED    98   6   7   6
  AMP PEAK 36(19Q12) WILD-TYPE 249  12  12  19
D36V11, multiclass
    clus
vv   AMP PEAK 36(19Q12) MUTATED AMP PEAK 36(19Q12) WILD-TYPE
  R0                         98                          249
  R1                          6                           12
  R2                          7                           12
  RX                          6                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(19Q12) MUTATED      43                         6
  AMP PEAK 36(19Q12) WILD-TYPE    86                         7
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 36(19Q12) MUTATED                                           1   107
  AMP PEAK 36(19Q12) WILD-TYPE                                         0   278
D36V13, multiclass
                                           clus
vv                                          AMP PEAK 36(19Q12) MUTATED
  ASIAN                                                             43
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            107
                                           clus
vv                                          AMP PEAK 36(19Q12) WILD-TYPE
  ASIAN                                                               86
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              278
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                              cls
clus                             0   1
  AMP PEAK 36(19Q12) MUTATED     2 119
  AMP PEAK 36(19Q12) WILD-TYPE   5 275
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 36(19Q12) MUTATED      2  119
  AMP PEAK 36(19Q12) WILD-TYPE    5  275
                        clus
vv                       AMP PEAK 36(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        119
                        clus
vv                       AMP PEAK 36(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          275
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 37(19Q13.43) MUTATION ANALYSIS
D37V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 37(19Q13.43) MUTATED    93  54
  AMP PEAK 37(19Q13.43) WILD-TYPE 261 167
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                            147                             428 
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                             54                             167 
$`AMP PEAK 37(19Q13.43) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL 
       58.55         7.63        13.94         8.94        16.24        20.09 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H 
       20.12         3.88        23.41        12.82         4.67        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE 
      122.10         3.68        23.18         3.16         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A88S 
        3.68         4.70        32.61         3.32         3.16         6.94 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       13.55         5.49        27.12        46.09        10.36         5.92 
TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ 
       15.35         0.10        12.00        12.03         0.13         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG 
       14.70         7.04        29.59        53.95         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-AA7I 
        7.00        20.38         3.42        15.35        28.11        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-B7-A5TK TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7716 
       10.16         2.10         9.47        19.33         9.21        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8286 
       28.73         3.45        12.76        18.71        12.26        12.95 
TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8678 TCGA-BR-8690 
        2.20         3.32         9.21         1.12        11.54        10.68 
TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 
        6.08         0.72        13.51        20.65        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48C 
        0.07         0.07         0.16         0.13         9.34        11.61 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4475 
       54.08         4.01        47.05        21.99        12.00        22.98 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 
        0.99         4.01        12.36        19.13        18.54        17.19 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU 
       10.55        11.31        12.33        24.72        21.14        16.44 
TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 
       13.78         9.76         2.96        16.24        72.23         3.48 
TCGA-FP-7916 TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       14.07         5.52        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 
       12.10        10.62        24.30        22.75         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP 
       12.95         9.67        27.42         3.45         5.19         6.44 
TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT 
        6.74        60.56        37.64         6.08        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 
        5.13        35.61         5.79        48.79        13.25         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19        12.79         2.70        36.69         1.71        36.16 
TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        2.01         5.72        64.18        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-VQ-AA6K 
       22.09        16.14        12.43 

$`AMP PEAK 37(19Q13.43) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR 
       25.78        31.27        14.30         5.92         4.21        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS 
       18.64         9.30         0.53        17.03         0.79         9.96 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
       14.86        12.16        44.75        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ 
        6.28        30.25         0.30         4.31        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93        18.35         7.17         1.38        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49L 
       21.37         8.71        13.41        83.24        52.57        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       12.66        12.43        13.41         0.10        13.15         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.23        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XQ 
       33.11         5.16         7.82         8.02         7.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30        15.78         1.45        20.02         5.29         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         4.44        18.81        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-AAPN 
       46.19        15.06        11.24         9.17         3.42         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        32.94        12.82        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        18.15        15.32        12.43         9.07 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43        11.44         0.69         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56         2.66        16.31        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        12.56        13.87         7.53        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
       12.82         0.66        19.36         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-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-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        6.58        12.20         0.10        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       65.10        69.04        21.07         7.99        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.55        18.84        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       15.22        15.98        12.79        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        14.66        20.91        14.27         5.92        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 
       14.76        13.71        11.24        11.31        11.44        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       14.47        21.27        11.38        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-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-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       26.47         1.51         5.92         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84        12.30         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36        13.08         1.41 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52        61.25         4.60         9.24 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         9.50         9.73        52.24         9.04        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        4.54         6.58         2.66        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       32.94        29.98        17.13        54.12        26.04        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                          122.1                           122.3 
  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE 
                          12.03                           13.08 
[1] "0.1 - 122.1 (12.0)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1"  
D37V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 37(19Q13.43) MUTATED         4        3       13        9        11
  AMP PEAK 37(19Q13.43) WILD-TYPE       7       16       35       23        66
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 37(19Q13.43) MUTATED          22         8         27         22
  AMP PEAK 37(19Q13.43) WILD-TYPE        62        21         70         50
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 37(19Q13.43) MUTATED            9       13         2
  AMP PEAK 37(19Q13.43) WILD-TYPE         39       38         2
D37V3, multiclass
            clus
vv           AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  STAGE I                                4                               7
  STAGE IA                               3                              16
  STAGE IB                              13                              35
  STAGE II                               9                              23
  STAGE IIA                             11                              66
  STAGE IIB                             22                              62
  STAGE III                              8                              21
  STAGE IIIA                            27                              70
  STAGE IIIB                            22                              50
  STAGE IIIC                             9                              39
  STAGE IV                              13                              38
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 37(19Q13.43) MUTATED      13  28  80  25
  AMP PEAK 37(19Q13.43) WILD-TYPE    40  98 200  99
D37V4, multiclass
       clus
vv      AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  T0+T1                            13                              40
  T2                               28                              98
  T3                               80                             200
  T4                               25                              99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 37(19Q13.43) MUTATED    45  45  23  31
  AMP PEAK 37(19Q13.43) WILD-TYPE 155 137  73  66
D37V5, multiclass
    clus
vv   AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  N0                            45                             155
  N1                            45                             137
  N2                            23                              73
  N3                            31                              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"
D37V6, binary
                                 cls
clus                                0   1
  AMP PEAK 37(19Q13.43) MUTATED   125  10
  AMP PEAK 37(19Q13.43) WILD-TYPE 388  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 37(19Q13.43) MUTATED    125   10
  AMP PEAK 37(19Q13.43) WILD-TYPE  388   29
   clus
vv  AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  0                           125                             388
  1                            10                              29
[1] 2 2
[1] FALSE
D37V7, binary
                                 cls
clus                                0   1
  AMP PEAK 37(19Q13.43) MUTATED    42 115
  AMP PEAK 37(19Q13.43) WILD-TYPE 140 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 37(19Q13.43) MUTATED     42  115
  AMP PEAK 37(19Q13.43) WILD-TYPE  140  312
        clus
vv       AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  FEMALE                            42                             140
  MALE                             115                             312
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 37(19Q13.43) MUTATED                                      21
  AMP PEAK 37(19Q13.43) WILD-TYPE                                    50
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 37(19Q13.43) MUTATED                                                       34
  AMP PEAK 37(19Q13.43) WILD-TYPE                                                    128
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 37(19Q13.43) MUTATED                                                                  19
  AMP PEAK 37(19Q13.43) WILD-TYPE                                                                62
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 37(19Q13.43) MUTATED                                                 21
  AMP PEAK 37(19Q13.43) WILD-TYPE                                               57
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 37(19Q13.43) MUTATED                                                          4
  AMP PEAK 37(19Q13.43) WILD-TYPE                                                       17
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 37(19Q13.43) MUTATED                                                           2
  AMP PEAK 37(19Q13.43) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 37(19Q13.43) MUTATED                                          4
  AMP PEAK 37(19Q13.43) WILD-TYPE                                        9
D37V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 37(19Q13.43) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  AMP PEAK 37(19Q13.43) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                                 cls
clus                                0   1
  AMP PEAK 37(19Q13.43) MUTATED     4 153
  AMP PEAK 37(19Q13.43) WILD-TYPE   2 450
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 37(19Q13.43) MUTATED      4  153
  AMP PEAK 37(19Q13.43) WILD-TYPE    2  450
     clus
vv    AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  NO                              4                               2
  YES                           153                             450
[1] 2 2
[1] FALSE
D37V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 37(19Q13.43) MUTATED    85   6   7   4
  AMP PEAK 37(19Q13.43) WILD-TYPE 262  12  12  21
D37V11, multiclass
    clus
vv   AMP PEAK 37(19Q13.43) MUTATED AMP PEAK 37(19Q13.43) WILD-TYPE
  R0                            85                             262
  R1                             6                              12
  R2                             7                              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"
D37V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 37(19Q13.43) MUTATED      38                         6
  AMP PEAK 37(19Q13.43) WILD-TYPE    91                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 37(19Q13.43) MUTATED                                           1
  AMP PEAK 37(19Q13.43) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 37(19Q13.43) MUTATED      88
  AMP PEAK 37(19Q13.43) WILD-TYPE   297
D37V13, multiclass
                                           clus
vv                                          AMP PEAK 37(19Q13.43) MUTATED
  ASIAN                                                                38
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                88
                                           clus
vv                                          AMP PEAK 37(19Q13.43) WILD-TYPE
  ASIAN                                                                  91
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 297
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                                 cls
clus                                0   1
  AMP PEAK 37(19Q13.43) MUTATED     1 101
  AMP PEAK 37(19Q13.43) WILD-TYPE   6 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 37(19Q13.43) MUTATED      1  101
  AMP PEAK 37(19Q13.43) WILD-TYPE    6  293
                        clus
vv                       AMP PEAK 37(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           101
                        clus
vv                       AMP PEAK 37(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             293
[1] 2 2
[1] FALSE

Clustering(38) Variable = AMP PEAK 38(20Q13.2) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 38(20Q13.2) MUTATED   235 155
  AMP PEAK 38(20Q13.2) WILD-TYPE 119  66
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                           390                            185 
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                           155                             66 
$`AMP PEAK 38(20Q13.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        0.79        23.41         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       44.75         3.68        21.70        23.18        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
        3.16        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        3.68         4.70        32.61        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        7.43         6.94         2.60         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        35.97        12.92        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
       46.09        10.36        10.45         0.10        13.15         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.25         0.10        12.59        12.49        12.76         0.10 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.02         5.29         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         4.44        19.96        22.82         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JE 
       28.11        42.87        46.19        11.24         9.17         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6453 
        6.97         4.64        18.35        30.90         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-7196 
        9.17        18.05        19.89        21.11        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.24        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
       28.73         3.45        12.76        18.71        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.69         9.60         0.56         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       15.58         7.40        14.04        14.79         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 
       25.18         9.21        20.22        15.81         9.34         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         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       10.68        13.87         7.53        22.26         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.72         0.53        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 
        1.15        13.64         3.25        13.15        13.18         0.07 
TCGA-CD-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-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.13         0.13         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         7.99         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-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 
       18.97         7.07        12.00        22.98        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99        12.03        15.02        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       19.13        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44         5.92        15.16        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A 
       11.31         9.76         2.96        15.65         8.38         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        0.62         7.99        16.24        14.47        72.23        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 
        3.48        19.53        14.07        22.29        17.06         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52         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 
       23.84        12.30         9.67         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
        3.45         3.39        18.38         5.19         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW 
        8.52        61.25         6.08         8.61        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
      115.69        57.44         8.94        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       21.73        46.26        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       17.85         1.87        15.65        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       65.16        36.69        11.93        18.74        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        2.01         4.54         5.72        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        18.41        40.08        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        21.11        12.43        10.62         0.79 

$`AMP PEAK 38(20Q13.2) WILD-TYPE`
TCGA-2H-A9GL TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
        5.92         6.21        20.09        20.78        18.64         9.30 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG 
       12.82         9.96        14.86        60.39        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ 
       42.77        25.41        24.03         6.28        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NK 
       47.93         8.71        25.12         7.40        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
        7.76        83.24         5.92        12.66        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       15.35        12.46        12.59        22.39        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.33        13.22         4.47        10.52        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER 
        7.82         1.45        20.38        15.35        18.81        12.43 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR 
       18.31        30.71        18.18        15.06        15.91        10.16 
TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4267 
        3.42        26.70        11.70        19.56         7.43         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 
        9.57        34.68        32.78        25.61        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 
       30.90        31.20        24.76        23.93        12.43         9.07 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 
       17.49        12.26        20.55         8.05        12.95         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
       26.33         4.31         3.32        11.80        19.17        15.85 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 
        3.72         1.12        12.79        13.45         6.28        15.81 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       12.56         6.08        13.41        13.51         8.98        14.17 
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-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ 
        0.30         0.07         0.10         0.10        11.31        12.62 
TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
        1.02         0.00         9.01         6.97         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
      105.07        65.10        21.07        18.61        17.85        10.55 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 
       17.19        18.21        13.78        14.76        11.44         4.34 
TCGA-D7-A74B TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB 
        7.13        21.27        59.54         5.03        13.58        18.08 
TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.41         5.59        11.84        24.20        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
        6.51        19.36         8.88        18.81         5.36        13.08 
TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 
        6.44         6.51         7.82         3.72        19.73         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        9.24        11.05         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       71.38        16.87        19.04        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP 
        7.73        28.96        34.29        16.31         9.27        23.41 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 
       13.35        26.24        11.70        61.22        20.81        55.43 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6I 
        6.58         2.66        22.09        28.41        16.14 

  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                         122.1                          122.3 
  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE 
                         12.46                          13.35 
[1] "0.1 - 122.1 (12.5)" "0.0 - 122.3 (13.3)"
[1] "hr=" "1.3"
D38V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 38(20Q13.2) MUTATED         8       13       29       19        46
  AMP PEAK 38(20Q13.2) WILD-TYPE       3        6       19       13        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 38(20Q13.2) MUTATED          57        22         72         48
  AMP PEAK 38(20Q13.2) WILD-TYPE        27         7         25         24
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 38(20Q13.2) MUTATED           28       32         4
  AMP PEAK 38(20Q13.2) WILD-TYPE         20       19         0
D38V3, multiclass
            clus
vv           AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  STAGE I                               8                              3
  STAGE IA                             13                              6
  STAGE IB                             29                             19
  STAGE II                             19                             13
  STAGE IIA                            46                             31
  STAGE IIB                            57                             27
  STAGE III                            22                              7
  STAGE IIIA                           72                             25
  STAGE IIIB                           48                             24
  STAGE IIIC                           28                             20
  STAGE IV                             32                             19
  STAGE IVA                             4                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 38(20Q13.2) MUTATED      36  82 195  73
  AMP PEAK 38(20Q13.2) WILD-TYPE    17  44  85  51
D38V4, multiclass
       clus
vv      AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  T0+T1                           36                             17
  T2                              82                             44
  T3                             195                             85
  T4                              73                             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
  AMP PEAK 38(20Q13.2) MUTATED   118 134  68  60
  AMP PEAK 38(20Q13.2) WILD-TYPE  82  48  28  37
D38V5, multiclass
    clus
vv   AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  N0                          118                             82
  N1                          134                             48
  N2                           68                             28
  N3                           60                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                                cls
clus                               0   1
  AMP PEAK 38(20Q13.2) MUTATED   337  25
  AMP PEAK 38(20Q13.2) WILD-TYPE 176  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(20Q13.2) MUTATED    337   25
  AMP PEAK 38(20Q13.2) WILD-TYPE  176   14
   clus
vv  AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  0                          337                            176
  1                           25                             14
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                               0   1
  AMP PEAK 38(20Q13.2) MUTATED   105 302
  AMP PEAK 38(20Q13.2) WILD-TYPE  77 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(20Q13.2) MUTATED    105  302
  AMP PEAK 38(20Q13.2) WILD-TYPE   77  125
        clus
vv       AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  FEMALE                          105                             77
  MALE                            302                            125
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 38(20Q13.2) MUTATED                                      32
  AMP PEAK 38(20Q13.2) WILD-TYPE                                    39
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 38(20Q13.2) MUTATED                                                      101
  AMP PEAK 38(20Q13.2) WILD-TYPE                                                     61
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 38(20Q13.2) MUTATED                                                                  63
  AMP PEAK 38(20Q13.2) WILD-TYPE                                                                18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 38(20Q13.2) MUTATED                                                 64
  AMP PEAK 38(20Q13.2) WILD-TYPE                                               14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 38(20Q13.2) MUTATED                                                         13
  AMP PEAK 38(20Q13.2) WILD-TYPE                                                        8
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 38(20Q13.2) MUTATED                                                           6
  AMP PEAK 38(20Q13.2) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 38(20Q13.2) MUTATED                                          9
  AMP PEAK 38(20Q13.2) WILD-TYPE                                        4
D38V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 38(20Q13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            64
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     9
                                                                   clus
vv                                                                  AMP PEAK 38(20Q13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                                cls
clus                               0   1
  AMP PEAK 38(20Q13.2) MUTATED     4 403
  AMP PEAK 38(20Q13.2) WILD-TYPE   2 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(20Q13.2) MUTATED      4  403
  AMP PEAK 38(20Q13.2) WILD-TYPE    2  200
     clus
vv    AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  NO                             4                              2
  YES                          403                            200
[1] 2 2
[1] FALSE
D38V10, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 38(20Q13.2) MUTATED   236  10  13  14
  AMP PEAK 38(20Q13.2) WILD-TYPE 111   8   6  11
D38V11, multiclass
    clus
vv   AMP PEAK 38(20Q13.2) MUTATED AMP PEAK 38(20Q13.2) WILD-TYPE
  R0                          236                            111
  R1                           10                              8
  R2                           13                              6
  RX                           14                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 38(20Q13.2) MUTATED      85                        10
  AMP PEAK 38(20Q13.2) WILD-TYPE    44                         3
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 38(20Q13.2) MUTATED                                           1
  AMP PEAK 38(20Q13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 38(20Q13.2) MUTATED     250
  AMP PEAK 38(20Q13.2) WILD-TYPE   135
D38V13, multiclass
                                           clus
vv                                          AMP PEAK 38(20Q13.2) MUTATED
  ASIAN                                                               85
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              250
                                           clus
vv                                          AMP PEAK 38(20Q13.2) WILD-TYPE
  ASIAN                                                                 44
  BLACK OR AFRICAN AMERICAN                                              3
  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"
D38V14, binary
                                cls
clus                               0   1
  AMP PEAK 38(20Q13.2) MUTATED     6 252
  AMP PEAK 38(20Q13.2) WILD-TYPE   1 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(20Q13.2) MUTATED      6  252
  AMP PEAK 38(20Q13.2) WILD-TYPE    1  142
                        clus
vv                       AMP PEAK 38(20Q13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          252
                        clus
vv                       AMP PEAK 38(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE

Clustering(39) Variable = AMP PEAK 39(XQ28) MUTATION ANALYSIS
D39V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 39(XQ28) MUTATED    82  56
  AMP PEAK 39(XQ28) WILD-TYPE 272 165
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                        138                         437 
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                         56                         165 
$`AMP PEAK 39(XQ28) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
       14.30         5.92        16.24        20.09        20.78         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
        0.53        17.03        23.41        12.82         9.96         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A43J 
      122.10        44.75        25.41        23.18        30.25         4.31 
TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A8NK 
       24.00        19.99        47.93        18.35         1.38        13.55 
TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.10         0.10         0.10        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FO 
       22.39        13.22        25.25        12.00        13.18         0.13 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV 
        8.02        14.70        15.78         2.89        12.69        20.02 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        5.29        15.35         4.44        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD 
       18.18        42.87        46.19        11.24        15.91         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.10        19.73        11.70        11.01         9.44         6.61 
TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8362 
        4.64        19.33        21.11        18.15        14.43        13.08 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U 
        3.32        20.22         0.49        15.81         9.86        13.87 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
       22.26        12.89        14.17         1.15        13.64         0.07 
TCGA-CD-8527 TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4460 
        0.07         6.58        20.02         8.05        54.08        21.99 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 
        7.07        12.00         6.97        11.93        18.54        17.19 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
       15.98        12.33        14.66        15.16        11.24         9.76 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       15.65         7.40         0.62         7.99        72.23         3.48 
TCGA-FP-A8CX TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
        0.23        14.27        12.10        24.30        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 
       24.20        22.75        25.81        12.30         3.45         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-VQ-A8DT TCGA-VQ-A8P5 
        5.19         6.44        45.67        18.21        48.79         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       46.26        27.35        14.33        11.93        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       22.68         1.71        52.24        64.18        40.08        32.94 

$`AMP PEAK 39(XQ28) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 
        4.21        32.45         7.69         6.21        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP 
        2.63        20.12        18.64         9.30         0.79        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        3.16         0.30         8.94         3.68         4.70        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       21.01         3.32         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49         8.71        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       52.57        46.09        13.41        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.46        12.76         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 
        4.47        12.33        10.52        12.23        12.03        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        5.16         7.82         7.59         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW 
        6.35        53.95         9.30         1.45         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42         4.80         9.27        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       12.43         1.55        28.11        15.06         9.17        10.16 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4188 
        2.66        26.70        19.56         9.47         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-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-7722 
       24.76        35.24        23.93        15.42        28.01        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         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 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 
       13.45         6.28         7.53        11.54        16.44        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        8.22        10.68        12.56         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         8.98         0.72         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-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        3.42         9.34        11.31        12.43        11.61        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        7.99         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.55        18.84        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.22        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        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       16.44         5.92        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO 
       11.44         2.96         8.38         4.34         7.13        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       18.08        26.47         1.51         5.92        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH 
       11.41        10.62         0.76         5.59         3.25        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        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       35.61        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       27.88        32.48        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       23.41        15.65        13.35        26.24        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       36.69        11.70        61.22        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        5.72        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                       0.07                        0.00 
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                      122.1                       122.3 
  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE 
                      13.20                       12.59 
[1] "0.1 - 122.1 (13.2)" "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D39V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 39(XQ28) MUTATED         3        6        8        4        23
  AMP PEAK 39(XQ28) WILD-TYPE       8       13       40       28        54
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 39(XQ28) MUTATED          25         7         20         17
  AMP PEAK 39(XQ28) WILD-TYPE        59        22         77         55
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 39(XQ28) MUTATED            9       13         2
  AMP PEAK 39(XQ28) WILD-TYPE         39       38         2
D39V3, multiclass
            clus
vv           AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  STAGE I                            3                           8
  STAGE IA                           6                          13
  STAGE IB                           8                          40
  STAGE II                           4                          28
  STAGE IIA                         23                          54
  STAGE IIB                         25                          59
  STAGE III                          7                          22
  STAGE IIIA                        20                          77
  STAGE IIIB                        17                          55
  STAGE IIIC                         9                          39
  STAGE IV                          13                          38
  STAGE IVA                          2                           2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 39(XQ28) MUTATED      14  31  69  25
  AMP PEAK 39(XQ28) WILD-TYPE    39  95 211  99
D39V4, multiclass
       clus
vv      AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  T0+T1                        14                          39
  T2                           31                          95
  T3                           69                         211
  T4                           25                          99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 39(XQ28) MUTATED    51  43  23  20
  AMP PEAK 39(XQ28) WILD-TYPE 149 139  73  77
D39V5, multiclass
    clus
vv   AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  N0                        51                         149
  N1                        43                         139
  N2                        23                          73
  N3                        20                          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"
D39V6, binary
                             cls
clus                            0   1
  AMP PEAK 39(XQ28) MUTATED   118   9
  AMP PEAK 39(XQ28) WILD-TYPE 395  30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 39(XQ28) MUTATED    118    9
  AMP PEAK 39(XQ28) WILD-TYPE  395   30
   clus
vv  AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  0                       118                         395
  1                         9                          30
[1] 2 2
[1] FALSE
D39V7, binary
                             cls
clus                            0   1
  AMP PEAK 39(XQ28) MUTATED    35 111
  AMP PEAK 39(XQ28) WILD-TYPE 147 316
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 39(XQ28) MUTATED     35  111
  AMP PEAK 39(XQ28) WILD-TYPE  147  316
        clus
vv       AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  FEMALE                        35                         147
  MALE                         111                         316
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  AMP PEAK 39(XQ28) MUTATED                                       8
  AMP PEAK 39(XQ28) WILD-TYPE                                    63
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 39(XQ28) MUTATED                                                       29
  AMP PEAK 39(XQ28) WILD-TYPE                                                    133
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 39(XQ28) MUTATED                                                                  15
  AMP PEAK 39(XQ28) WILD-TYPE                                                                66
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  AMP PEAK 39(XQ28) MUTATED                                                 24
  AMP PEAK 39(XQ28) WILD-TYPE                                               54
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  AMP PEAK 39(XQ28) MUTATED                                                          1
  AMP PEAK 39(XQ28) WILD-TYPE                                                       20
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  AMP PEAK 39(XQ28) MUTATED                                                           2
  AMP PEAK 39(XQ28) WILD-TYPE                                                         6
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  AMP PEAK 39(XQ28) MUTATED                                          2
  AMP PEAK 39(XQ28) WILD-TYPE                                       11
D39V8, multiclass
                                                                   clus
vv                                                                  AMP PEAK 39(XQ28) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  2
                                                                   clus
vv                                                                  AMP PEAK 39(XQ28) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                             cls
clus                            0   1
  AMP PEAK 39(XQ28) MUTATED     0 146
  AMP PEAK 39(XQ28) WILD-TYPE   6 457
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 39(XQ28) MUTATED      0  146
  AMP PEAK 39(XQ28) WILD-TYPE    6  457
     clus
vv    AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  NO                          0                           6
  YES                       146                         457
[1] 2 2
[1] FALSE
D39V10, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 39(XQ28) MUTATED    65   2   2   5
  AMP PEAK 39(XQ28) WILD-TYPE 282  16  17  20
D39V11, multiclass
    clus
vv   AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  R0                        65                         282
  R1                         2                          16
  R2                         2                          17
  RX                         5                          20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 39(XQ28) MUTATED      42                         4
  AMP PEAK 39(XQ28) WILD-TYPE    87                         9
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 39(XQ28) MUTATED                                           0    85
  AMP PEAK 39(XQ28) WILD-TYPE                                         1   300
D39V13, multiclass
                                           clus
vv                                          AMP PEAK 39(XQ28) MUTATED
  ASIAN                                                            42
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            85
                                           clus
vv                                          AMP PEAK 39(XQ28) WILD-TYPE
  ASIAN                                                              87
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             300
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                             cls
clus                            0   1
  AMP PEAK 39(XQ28) MUTATED     3  97
  AMP PEAK 39(XQ28) WILD-TYPE   4 297
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 39(XQ28) MUTATED      3   97
  AMP PEAK 39(XQ28) WILD-TYPE    4  297
                        clus
vv                       AMP PEAK 39(XQ28) MUTATED AMP PEAK 39(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                        97                         297
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   111  82
  DEL PEAK  1(1P36.11) WILD-TYPE 243 139
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           193                            382 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            82                            139 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A4P3 
       16.24        32.45         7.69        33.27        20.09        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH 
        3.88         0.53        12.82       122.10        60.39        42.77 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       23.18         0.30         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        4.70         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         2.60         0.36         7.40         3.02        55.50 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS 
       35.97        12.92        16.47        13.22         5.49        13.41 
TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
        5.92         0.10        13.25        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 
       12.03        13.18         8.02         7.59         5.06         2.89 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45        20.38         3.42         4.80         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ 
       30.71        42.87         2.66        19.73        26.70        11.01 
TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 
        9.44        18.35         6.18         9.57        17.29        19.33 
TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8483 
        9.17        35.24        18.71        11.44         2.66         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
       25.18         9.21         0.49        11.54         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        7.53        22.26        20.65        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        3.25         0.07         0.07         0.13         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.13         3.42         9.34        11.31        11.61        12.20 
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 
       18.21        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 
        7.99        16.24        11.38        17.06        13.58         5.52 
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-IN-AB1V TCGA-KB-A6F7 
       12.95        23.84        12.30        27.42         7.82        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64         9.86        18.21         6.08         9.24         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.67       122.30        35.61         0.92        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48         7.73        46.26        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91A TCGA-VQ-A91Q 
       17.85         1.87        13.35        27.35        36.69        20.81 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T 
        9.73        52.24         4.54        64.18        21.04        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6K 
       18.41        40.08        32.94        29.98        17.13        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA 
       25.78         5.92         4.21         6.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        20.12         9.30        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        9.96        14.86         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D 
       68.02         3.68        41.52        25.41        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH 
       25.22        24.03         6.28         3.16        30.25        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NF 
        1.38         6.94         8.71        25.12         3.95         2.66 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.48        13.55         7.76        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       83.24        52.57        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43        13.41        13.15        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.23         0.13        33.11         5.16         7.82 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV 
       15.78        12.69         7.00        20.02         5.29        15.35 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       18.81        18.31        18.18        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5818 
        9.17        15.91        10.16         3.42         2.10        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       19.56         9.47         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
       30.90         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        17.49        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56        12.95        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
       13.45         6.28         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 
        8.22        12.56        13.87         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-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 
       12.43         6.58         0.10        12.62        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        1.02         4.01        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       18.97        12.00        22.98         6.97        36.00         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85        13.35        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       10.55        11.31        16.80        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       13.71        11.24        11.44         9.76        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13        14.47        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        14.07        22.29        59.54         5.03         0.56 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
        0.23        18.08        26.47        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       19.36         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        1.41         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A5UG 
        1.81        13.51         2.53         5.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73        45.67         8.52        61.25         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       57.44         8.94        16.87        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       28.96        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        26.24        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.50         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6F 
        5.72         2.66        42.54        22.09        28.41        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       26.04        16.14        21.11        10.62 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        12.330                         12.855 
[1] "0.1 - 122.3 (12.3)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1.2"
D40V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         5        3       16       11        25
  DEL PEAK  1(1P36.11) WILD-TYPE       6       16       32       21        52
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          28        15         32         24
  DEL PEAK  1(1P36.11) WILD-TYPE        56        14         65         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED            9       17         2
  DEL PEAK  1(1P36.11) WILD-TYPE         39       34         2
D40V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              3                             16
  STAGE IB                             16                             32
  STAGE II                             11                             21
  STAGE IIA                            25                             52
  STAGE IIB                            28                             56
  STAGE III                            15                             14
  STAGE IIIA                           32                             65
  STAGE IIIB                           24                             48
  STAGE IIIC                            9                             39
  STAGE IV                             17                             34
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED      18  42  99  32
  DEL PEAK  1(1P36.11) WILD-TYPE    35  84 181  92
D40V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                           18                             35
  T2                              42                             84
  T3                              99                            181
  T4                              32                             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED    60  65  34  28
  DEL PEAK  1(1P36.11) WILD-TYPE 140 117  62  69
D40V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           60                            140
  N1                           65                            117
  N2                           34                             62
  N3                           28                             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"
D40V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   167  13
  DEL PEAK  1(1P36.11) WILD-TYPE 346  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    167   13
  DEL PEAK  1(1P36.11) WILD-TYPE  346   26
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          167                            346
  1                           13                             26
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    54 149
  DEL PEAK  1(1P36.11) WILD-TYPE 128 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     54  149
  DEL PEAK  1(1P36.11) WILD-TYPE  128  278
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           54                            128
  MALE                            149                            278
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  1(1P36.11) MUTATED                                      11
  DEL PEAK  1(1P36.11) WILD-TYPE                                    60
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                       42
  DEL PEAK  1(1P36.11) WILD-TYPE                                                    120
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                                  31
  DEL PEAK  1(1P36.11) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                 35
  DEL PEAK  1(1P36.11) WILD-TYPE                                               43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                          7
  DEL PEAK  1(1P36.11) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  1(1P36.11) MUTATED                                                           2
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  1(1P36.11) MUTATED                                          5
  DEL PEAK  1(1P36.11) WILD-TYPE                                        8
D40V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            35
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK  1(1P36.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              43
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3 200
  DEL PEAK  1(1P36.11) WILD-TYPE   3 403
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3  200
  DEL PEAK  1(1P36.11) WILD-TYPE    3  403
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             3                              3
  YES                          200                            403
[1] 2 2
[1] FALSE
D40V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    96   8   9   9
  DEL PEAK  1(1P36.11) WILD-TYPE 251  10  10  16
D40V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           96                            251
  R1                            8                             10
  R2                            9                             10
  RX                            9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.11) MUTATED      40                         5
  DEL PEAK  1(1P36.11) WILD-TYPE    89                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.11) MUTATED                                           1
  DEL PEAK  1(1P36.11) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.11) MUTATED     123
  DEL PEAK  1(1P36.11) WILD-TYPE   262
D40V13, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                               40
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              123
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 89
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                262
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     0 113
  DEL PEAK  1(1P36.11) WILD-TYPE   7 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      0  113
  DEL PEAK  1(1P36.11) WILD-TYPE    7  281
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            281
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    87  57
  DEL PEAK  2(1P13.2) WILD-TYPE 267 164
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          144                           431 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           57                           164 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       14.30         7.63        13.94         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       33.27        20.09         2.63        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE 
        0.79         4.67         3.68         0.30         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        4.70        32.61         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         0.36         7.40        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K 
       35.97        12.92        13.48        16.47        13.41         5.92 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       13.25        12.59        12.59        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6Y0 
       10.52        12.00        13.18        33.11         7.59        53.95 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
        2.89         1.45        20.38         3.42         9.27         4.44 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-AA4D TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-6456 
       12.43         8.12        46.19        11.01         9.44        17.29 
TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 
       35.24         3.45        18.71         2.66         2.20        14.04 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ 
        5.39         9.21        11.54         9.86         8.22        22.26 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       12.89         0.66        20.42         1.15        13.64         3.25 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
        0.30         0.07         0.10         0.13         0.13         3.42 
TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 
       11.31        12.20         3.02         7.99        54.08        29.98 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 
       18.97        22.98        12.03         4.01        11.93        20.55 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 
       18.54        17.19        10.26        15.22        12.79        24.72 
TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       19.50        11.31         9.76        15.65         7.40         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 
        7.99        16.24        19.53         5.52         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-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BT TCGA-VQ-A8DL 
       37.64         9.86        18.21         9.24         8.61         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ 
       48.79         5.46        13.25         7.73        22.19         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91Z 
       17.85         9.27        36.69        18.74        36.16        52.24 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6B TCGA-VQ-AA6K 
        4.54        21.04        11.24        18.41        29.98        12.43 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         5.92         8.94        16.24 
TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D 
        6.21         0.85        20.78        20.12         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39        68.02        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF TCGA-L5-A4OI 
        6.28         3.16        30.25         4.31         3.68        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       21.01        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
        3.16        58.59         8.71        25.12         3.95         3.02 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       27.12        83.24        52.57        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
        0.10         0.10        12.46        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX 
        0.10        15.52        12.33        13.22         4.47        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.03         0.13         5.16         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04        29.59         6.35         9.30        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00        20.02         5.29         4.80        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       18.81        19.96        22.82         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        42.87        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        13.41        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82        19.36        13.51         0.46        20.65 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
       11.57         5.13         2.83        13.15        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.10         9.34        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       21.99         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
      105.07        15.02        28.96        79.07        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        19.13        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        13.35        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 
       14.76        13.71        11.24        11.44         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         7.13        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        7.82        13.51         5.56        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        45.67         8.52        61.25         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       16.87        19.04         5.79        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP 
       46.26        16.31         2.50        12.79         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       65.16        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 
        1.71         7.36         9.50         9.73         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        64.18         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        40.08        28.41        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        10.62         0.79 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         55.5                         122.3 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       11.425                        13.150 
[1] "0.1 - 55.5 (11.4)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        2       11        7        23
  DEL PEAK  2(1P13.2) WILD-TYPE       9       17       37       25        54
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          22        12         25         18
  DEL PEAK  2(1P13.2) WILD-TYPE        62        17         72         54
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  2(1P13.2) MUTATED            4       11         1
  DEL PEAK  2(1P13.2) WILD-TYPE         44       40         3
D41V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             2                            17
  STAGE IB                            11                            37
  STAGE II                             7                            25
  STAGE IIA                           23                            54
  STAGE IIB                           22                            62
  STAGE III                           12                            17
  STAGE IIIA                          25                            72
  STAGE IIIB                          18                            54
  STAGE IIIC                           4                            44
  STAGE IV                            11                            40
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  2(1P13.2) MUTATED      11  28  81  21
  DEL PEAK  2(1P13.2) WILD-TYPE    42  98 199 103
D41V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                          11                            42
  T2                             28                            98
  T3                             81                           199
  T4                             21                           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  2(1P13.2) MUTATED    48  45  30  15
  DEL PEAK  2(1P13.2) WILD-TYPE 152 137  66  82
D41V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          48                           152
  N1                          45                           137
  N2                          30                            66
  N3                          15                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED   125   9
  DEL PEAK  2(1P13.2) WILD-TYPE 388  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED    125    9
  DEL PEAK  2(1P13.2) WILD-TYPE  388   30
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                         125                           388
  1                           9                            30
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    35 115
  DEL PEAK  2(1P13.2) WILD-TYPE 147 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     35  115
  DEL PEAK  2(1P13.2) WILD-TYPE  147  312
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          35                           147
  MALE                           115                           312
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  2(1P13.2) MUTATED                                       7
  DEL PEAK  2(1P13.2) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                       30
  DEL PEAK  2(1P13.2) WILD-TYPE                                                    132
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.2) MUTATED                                                                  22
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                 24
  DEL PEAK  2(1P13.2) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                          4
  DEL PEAK  2(1P13.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                           1
  DEL PEAK  2(1P13.2) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  2(1P13.2) MUTATED                                          3
  DEL PEAK  2(1P13.2) WILD-TYPE                                       10
D41V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  2(1P13.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     1 149
  DEL PEAK  2(1P13.2) WILD-TYPE   5 454
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1  149
  DEL PEAK  2(1P13.2) WILD-TYPE    5  454
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                            1                             5
  YES                         149                           454
[1] 2 2
[1] FALSE
D41V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.2) MUTATED    68   4   7   3
  DEL PEAK  2(1P13.2) WILD-TYPE 279  14  12  22
D41V11, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  R0                          68                           279
  R1                           4                            14
  R2                           7                            12
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED      33                         2
  DEL PEAK  2(1P13.2) WILD-TYPE    96                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    92
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   293
D41V13, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              92
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                96
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     0  91
  DEL PEAK  2(1P13.2) WILD-TYPE   7 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0   91
  DEL PEAK  2(1P13.2) WILD-TYPE    7  303
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    23  20
  DEL PEAK  3(1Q44) WILD-TYPE 331 201
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         43                         532 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         20                         201 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A8NG 
        4.21         3.88       122.10        24.00        21.01        35.97 
TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-R6-A6DQ 
       83.24         5.92        13.41        12.46        22.39         7.59 
TCGA-R6-A6Y0 TCGA-VR-A8ER TCGA-VR-AA7D TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-7704 
       53.95        12.43         9.17         9.44        17.29        35.24 
TCGA-BR-8362 TCGA-BR-A452 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-A486 TCGA-CD-A48A 
       13.08         7.53        20.65        13.18         3.42        12.43 
TCGA-CD-A4MH TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5724 
       12.20         1.02        14.01        18.97         7.07        12.03 
TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 
       20.55        14.66        15.65        12.10         8.98         2.10 
TCGA-IN-8663 TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-VQ-A8PM 
        3.39         1.81         2.53         5.56        37.64         1.87 
TCGA-VQ-A91V 
       36.16 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       13.94         8.94        16.24        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
        6.28         3.16        30.25         0.30         4.31         8.94 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68         4.70        32.61        19.99        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        3.32         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        12.59         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         5.16         7.82         8.02         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.91        10.16         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       15.42        28.01        18.15        15.32        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.13         0.10         9.34        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         7.99         8.05        54.08         4.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       12.36        12.66        11.93        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 
       12.59         6.51         5.56         7.82        13.51        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU 
        9.27        23.41        15.65        13.35        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
        4.54         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      122.1                       122.3 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      12.43                       12.79 
[1] "1.0 - 122.1 (12.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D42V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(1Q44) MUTATED         2        0        2        1        10
  DEL PEAK  3(1Q44) WILD-TYPE       9       19       46       31        67
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           5         3          5          5
  DEL PEAK  3(1Q44) WILD-TYPE        79        26         92         67
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(1Q44) MUTATED            5        4         0
  DEL PEAK  3(1Q44) WILD-TYPE         43       47         4
D42V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            2                           9
  STAGE IA                           0                          19
  STAGE IB                           2                          46
  STAGE II                           1                          31
  STAGE IIA                         10                          67
  STAGE IIB                          5                          79
  STAGE III                          3                          26
  STAGE IIIA                         5                          92
  STAGE IIIB                         5                          67
  STAGE IIIC                         5                          43
  STAGE IV                           4                          47
  STAGE IVA                          0                           4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  DEL PEAK  3(1Q44) MUTATED       2   8  24   8
  DEL PEAK  3(1Q44) WILD-TYPE    51 118 256 116
D42V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         2                          51
  T2                            8                         118
  T3                           24                         256
  T4                            8                         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"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  3(1Q44) MUTATED    15   9   8   9
  DEL PEAK  3(1Q44) WILD-TYPE 185 173  88  88
D42V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        15                         185
  N1                         9                         173
  N2                         8                          88
  N3                         9                          88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    39   2
  DEL PEAK  3(1Q44) WILD-TYPE 474  37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     39    2
  DEL PEAK  3(1Q44) WILD-TYPE  474   37
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        39                         474
  1                         2                          37
[1] 2 2
[1] FALSE
D42V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    13  32
  DEL PEAK  3(1Q44) WILD-TYPE 169 395
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     13   32
  DEL PEAK  3(1Q44) WILD-TYPE  169  395
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        13                         169
  MALE                          32                         395
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  3(1Q44) MUTATED                                       4
  DEL PEAK  3(1Q44) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                       14
  DEL PEAK  3(1Q44) WILD-TYPE                                                    148
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(1Q44) MUTATED                                                                   5
  DEL PEAK  3(1Q44) WILD-TYPE                                                                76
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  3(1Q44) MUTATED                                                  6
  DEL PEAK  3(1Q44) WILD-TYPE                                               72
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  3(1Q44) MUTATED                                                          0
  DEL PEAK  3(1Q44) WILD-TYPE                                                       21
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  3(1Q44) MUTATED                                                           0
  DEL PEAK  3(1Q44) WILD-TYPE                                                         8
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  3(1Q44) MUTATED                                          1
  DEL PEAK  3(1Q44) WILD-TYPE                                       12
D42V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  1
                                                                   clus
vv                                                                  DEL PEAK  3(1Q44) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  45
  DEL PEAK  3(1Q44) WILD-TYPE   6 558
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   45
  DEL PEAK  3(1Q44) WILD-TYPE    6  558
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        45                         558
[1] 2 2
[1] FALSE
D42V10, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  3(1Q44) MUTATED    22   1   2   1
  DEL PEAK  3(1Q44) WILD-TYPE 325  17  17  24
D42V11, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  R0                        22                         325
  R1                         1                          17
  R2                         2                          17
  RX                         1                          24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q44) MUTATED      13                         0
  DEL PEAK  3(1Q44) WILD-TYPE   116                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q44) MUTATED                                           0    22
  DEL PEAK  3(1Q44) WILD-TYPE                                         1   363
D42V13, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            22
                                           clus
vv                                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                                             116
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  28
  DEL PEAK  3(1Q44) WILD-TYPE   7 366
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   28
  DEL PEAK  3(1Q44) WILD-TYPE    7  366
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           7
  NOT HISPANIC OR LATINO                        28                         366
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  4(1Q44) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q44) MUTATED    24  18
  DEL PEAK  4(1Q44) WILD-TYPE 330 203
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         42                         533 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         18                         203 
$`DEL PEAK  4(1Q44) MUTATED`
TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OE TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A8NG 
        3.88         9.96        24.00        21.01         3.32        35.97 
TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 
       83.24        10.36         5.92        13.41        12.46        22.39 
TCGA-LN-A7HW TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-VR-A8ER TCGA-VR-AA7D TCGA-B7-A5TN 
       12.00         7.59        53.95        12.43         9.17         9.44 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6705 TCGA-BR-7704 TCGA-BR-8077 TCGA-BR-8362 
       17.29        19.33        25.61        35.24         0.69        13.08 
TCGA-BR-A4PD TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4441 TCGA-CG-5724 TCGA-D7-6519 
       20.65         3.42        12.43        14.01        12.03        20.55 
TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-IN-8663 
       14.66        15.65        12.10         8.98         2.10         3.39 
TCGA-IN-A6RI TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8P3 TCGA-VQ-A91V TCGA-VQ-A928 
       18.38         2.53        37.64        32.48        36.16         5.72 

$`DEL PEAK  4(1Q44) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         9.30         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       42.77        25.41        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM 
        8.94         3.68         4.70        32.61        19.99        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         7.17         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       52.57        46.09        10.45        12.66        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       13.15        15.35         0.10        13.25         0.10        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.23        12.03        13.18         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35         9.30        15.78         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        7.00        20.02        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       42.87        46.19        15.06        11.24        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
        3.42         2.10         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-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        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.73        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43        11.44        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
       15.58         7.40         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-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56        13.87         7.53         6.08        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-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 
        9.34        11.31        11.61         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        7.99        12.36        12.66        11.93        19.13        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-D7-6815 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-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        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-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-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-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26        12.95        19.36        23.84        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-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         4.54         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
        2.66        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                       0.69                        0.00 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      83.24                      122.30 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                      12.77                       12.76 
[1] "0.7 - 83.2 (12.8)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D43V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(1Q44) MUTATED         2        0        1        1        10
  DEL PEAK  4(1Q44) WILD-TYPE       9       19       47       31        67
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q44) MUTATED           7         2          3          7
  DEL PEAK  4(1Q44) WILD-TYPE        77        27         94         65
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(1Q44) MUTATED            6        2         0
  DEL PEAK  4(1Q44) WILD-TYPE         42       49         4
D43V3, multiclass
            clus
vv           DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  STAGE I                            2                           9
  STAGE IA                           0                          19
  STAGE IB                           1                          47
  STAGE II                           1                          31
  STAGE IIA                         10                          67
  STAGE IIB                          7                          77
  STAGE III                          2                          27
  STAGE IIIA                         3                          94
  STAGE IIIB                         7                          65
  STAGE IIIC                         6                          42
  STAGE IV                           2                          49
  STAGE IVA                          0                           4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  DEL PEAK  4(1Q44) MUTATED       2   9  22   8
  DEL PEAK  4(1Q44) WILD-TYPE    51 117 258 116
D43V4, multiclass
       clus
vv      DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  T0+T1                         2                          51
  T2                            9                         117
  T3                           22                         258
  T4                            8                         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"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  4(1Q44) MUTATED    14  10   6  10
  DEL PEAK  4(1Q44) WILD-TYPE 186 172  90  87
D43V5, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  N0                        14                         186
  N1                        10                         172
  N2                         6                          90
  N3                        10                          87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    37   1
  DEL PEAK  4(1Q44) WILD-TYPE 476  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     37    1
  DEL PEAK  4(1Q44) WILD-TYPE  476   38
   clus
vv  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  0                        37                         476
  1                         1                          38
[1] 2 2
[1] FALSE
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    14  29
  DEL PEAK  4(1Q44) WILD-TYPE 168 398
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     14   29
  DEL PEAK  4(1Q44) WILD-TYPE  168  398
        clus
vv       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  FEMALE                        14                         168
  MALE                          29                         398
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  4(1Q44) MUTATED                                       4
  DEL PEAK  4(1Q44) WILD-TYPE                                    67
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                       12
  DEL PEAK  4(1Q44) WILD-TYPE                                                    150
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(1Q44) MUTATED                                                                   3
  DEL PEAK  4(1Q44) WILD-TYPE                                                                78
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  4(1Q44) MUTATED                                                  6
  DEL PEAK  4(1Q44) WILD-TYPE                                               72
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  4(1Q44) MUTATED                                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                                       21
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  4(1Q44) MUTATED                                                           1
  DEL PEAK  4(1Q44) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  4(1Q44) MUTATED                                          0
  DEL PEAK  4(1Q44) WILD-TYPE                                       13
D43V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  0
                                                                   clus
vv                                                                  DEL PEAK  4(1Q44) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    150
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          78
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           72
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   13
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  43
  DEL PEAK  4(1Q44) WILD-TYPE   6 560
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   43
  DEL PEAK  4(1Q44) WILD-TYPE    6  560
     clus
vv    DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  NO                          0                           6
  YES                        43                         560
[1] 2 2
[1] FALSE
D43V10, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q44) MUTATED    22   0   1   0
  DEL PEAK  4(1Q44) WILD-TYPE 325  18  18  25
D43V11, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  R0                        22                         325
  R1                         0                          18
  R2                         1                          18
  RX                         0                          25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(1Q44) MUTATED      11                         0
  DEL PEAK  4(1Q44) WILD-TYPE   118                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(1Q44) MUTATED                                           0    27
  DEL PEAK  4(1Q44) WILD-TYPE                                         1   358
D43V13, multiclass
                                           clus
vv                                          DEL PEAK  4(1Q44) MUTATED
  ASIAN                                                            11
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            27
                                           clus
vv                                          DEL PEAK  4(1Q44) WILD-TYPE
  ASIAN                                                             118
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  30
  DEL PEAK  4(1Q44) WILD-TYPE   7 364
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   30
  DEL PEAK  4(1Q44) WILD-TYPE    7  364
                        clus
vv                       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                           7
  NOT HISPANIC OR LATINO                        30                         364
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    62  52
  DEL PEAK  5(2Q22.1) WILD-TYPE 292 169
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          114                           461 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           52                           169 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       58.55         4.21        33.27         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 
       18.64         0.53        17.03         0.79         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-L5-A43C TCGA-L5-A43H 
       12.16        44.75        68.02        41.52         3.16         0.30 
TCGA-L5-A4OE TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NK 
       24.00        58.59         7.43         7.40         3.02        13.55 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A5U5 
       52.57        10.36        10.45        12.46        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        10.52        12.00        12.23        13.18         0.13 
TCGA-Q9-A6FU TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB 
        5.16        29.59        53.95         2.89        20.38         5.29 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43        18.31         8.12        30.71        18.18        42.87 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-BR-4183 TCGA-BR-4188 
       11.24        15.91         3.42         2.66         6.61         7.43 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8369 TCGA-BR-8483 
       19.33         9.17        28.73         0.69        14.04         5.39 
TCGA-BR-8484 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-8535 TCGA-CD-A486 
       25.18         8.22         0.66        20.65         0.13         3.42 
TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5720 
       12.43        20.02        47.05        18.97        22.98         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
      105.07        12.03        15.02        12.66        11.93        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6F0 TCGA-EQ-5647 
       17.19        10.26        24.72        14.66         2.96         0.62 
TCGA-EQ-A4SO TCGA-F1-A72C TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD 
       16.24        11.38        26.47        22.75         6.25        27.42 
TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H TCGA-MX-A663 
       18.38         1.41         6.51         7.82        37.64         9.86 
TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DZ 
       18.21        16.67       115.69        35.61         0.92        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A91D TCGA-VQ-A91N 
       18.48         7.73         2.70        27.35        11.70        18.74 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A 
       52.24         9.04        42.54        22.09        40.08        32.94 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69         6.21        20.09 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
       20.78         3.88         9.30        23.41        12.82        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 
       14.50       122.10        60.39         3.68        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         4.31         8.94         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE 
        8.71         2.60        25.12         0.36         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        7.76         5.49        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-M9-A5M8 
       15.52        11.54        13.22        25.25        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.02         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4D 
       18.81        19.96        22.82         1.55        28.11        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 
       15.06         9.17        10.16         2.10        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 
       11.70        19.56        11.01         9.47         9.44         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        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-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        14.43        11.44        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-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-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
       12.82        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-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         9.34        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 
       69.04        21.07         7.99        12.36        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        18.21        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40         7.13         7.99        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        23.84        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         6.44         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         1.81        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15         3.72        19.73        45.67         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        16.87        19.04         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        26.24        64.57        14.33        65.16        36.69 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.50         9.73         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T 
        6.58         5.72        64.18        21.04         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       12.445                        12.790 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q22.1) MUTATED         3        2        9        4        22
  DEL PEAK  5(2Q22.1) WILD-TYPE       8       17       39       28        55
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q22.1) MUTATED          16         6         18         13
  DEL PEAK  5(2Q22.1) WILD-TYPE        68        23         79         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(2Q22.1) MUTATED            7       12         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         41       39         4
D44V3, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             2                            17
  STAGE IB                             9                            39
  STAGE II                             4                            28
  STAGE IIA                           22                            55
  STAGE IIB                           16                            68
  STAGE III                            6                            23
  STAGE IIIA                          18                            79
  STAGE IIIB                          13                            59
  STAGE IIIC                           7                            41
  STAGE IV                            12                            39
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  5(2Q22.1) MUTATED       9  27  56  21
  DEL PEAK  5(2Q22.1) WILD-TYPE    44  99 224 103
D44V4, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                           9                            44
  T2                             27                            99
  T3                             56                           224
  T4                             21                           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  5(2Q22.1) MUTATED    42  38  18  16
  DEL PEAK  5(2Q22.1) WILD-TYPE 158 144  78  81
D44V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          42                           158
  N1                          38                           144
  N2                          18                            78
  N3                          16                            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    99   8
  DEL PEAK  5(2Q22.1) WILD-TYPE 414  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     99    8
  DEL PEAK  5(2Q22.1) WILD-TYPE  414   31
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          99                           414
  1                           8                            31
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    35  83
  DEL PEAK  5(2Q22.1) WILD-TYPE 147 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     35   83
  DEL PEAK  5(2Q22.1) WILD-TYPE  147  344
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          35                           147
  MALE                            83                           344
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                       9
  DEL PEAK  5(2Q22.1) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q22.1) MUTATED                                                       25
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                    137
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q22.1) MUTATED                                                                  10
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                                71
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                                 15
  DEL PEAK  5(2Q22.1) WILD-TYPE                                               63
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                                          2
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                                           1
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                          3
  DEL PEAK  5(2Q22.1) WILD-TYPE                                       10
D44V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  5(2Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  5(2Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            71
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     2 116
  DEL PEAK  5(2Q22.1) WILD-TYPE   4 487
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      2  116
  DEL PEAK  5(2Q22.1) WILD-TYPE    4  487
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                            2                             4
  YES                         116                           487
[1] 2 2
[1] FALSE
D44V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q22.1) MUTATED    53   4   4   2
  DEL PEAK  5(2Q22.1) WILD-TYPE 294  14  15  23
D44V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          53                           294
  R1                           4                            14
  R2                           4                            15
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q22.1) MUTATED      26                         2
  DEL PEAK  5(2Q22.1) WILD-TYPE   103                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q22.1) MUTATED                                           0    72
  DEL PEAK  5(2Q22.1) WILD-TYPE                                         1   313
D44V13, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q22.1) MUTATED
  ASIAN                                                              26
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              72
                                           clus
vv                                          DEL PEAK  5(2Q22.1) WILD-TYPE
  ASIAN                                                               103
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     1  69
  DEL PEAK  5(2Q22.1) WILD-TYPE   6 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      1   69
  DEL PEAK  5(2Q22.1) WILD-TYPE    6  325
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           325
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK  6(2Q32.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q32.1) MUTATED    45  34
  DEL PEAK  6(2Q32.1) WILD-TYPE 309 187
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           79                           496 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           34                           187 
$`DEL PEAK  6(2Q32.1) MUTATED`
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A43H 
        0.85        20.12        18.64         0.79        68.02         0.30 
TCGA-L5-A4OS TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NV 
       58.59         0.36         3.02        16.47        13.55        52.57 
TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.41        12.46        12.33        10.52        12.23        13.18 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-VR-A8Q7 TCGA-ZR-A9CJ TCGA-BR-4188 TCGA-BR-6456 
        2.89         1.45        42.87        19.73         7.43        17.29 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       19.33         9.17        17.49         0.69         9.60        12.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8676 TCGA-BR-8682 
       26.33         4.31        14.04         3.32         7.53        16.44 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-8525 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A486 
        8.22        20.65         0.07         0.10         0.13         3.42 
TCGA-CG-4300 TCGA-CG-4444 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5724 
       20.02        47.05         0.00        12.00         0.99        12.03 
TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-8575 TCGA-D7-8576 
       15.02        12.66        11.93        17.19        18.21        14.66 
TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GU 
        2.96        26.47         5.92         5.59        22.75         6.25 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-AB1V TCGA-MX-A663 TCGA-R5-A7ZE TCGA-RD-A7C1 
       27.42        18.38         7.82         9.86        18.21        16.67 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PU 
        0.92        13.25        13.02        32.48        17.85        27.35 
TCGA-VQ-A8PY TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A 
       14.33         9.73        21.04        22.09        40.08        32.94 
TCGA-ZA-A8F6 
       10.62 

$`DEL PEAK  6(2Q32.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS 
        6.21        33.27        20.09        20.78         2.63         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        9.30         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       27.12        83.24        46.09        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43         0.10        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       12.33        25.25        12.00        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       12.69         7.00        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        4.80        15.35         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       22.82        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 
       15.91        10.16         3.42         2.10         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         4.64        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       12.76        18.71        14.43        11.44        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       17.52         0.95        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
        0.49        11.54        15.81         9.86        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-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-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         9.34        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20         0.10        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        1.02         6.02         0.99       105.07        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        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-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.99        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       18.08         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76        24.30        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        21.21         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
       60.56        20.15        37.64         3.72        19.73        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       19.04         5.79        48.79         5.46        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        64.18         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        21.11        12.43         0.79 

  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                       13.020                        12.725 
[1] "0.0 - 68.0 (13.0)"  "0.1 - 122.3 (12.7)"
[1] "hr=" "1.2"
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q32.1) MUTATED         2        1        9        3        11
  DEL PEAK  6(2Q32.1) WILD-TYPE       9       18       39       29        66
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q32.1) MUTATED          11         3         14         10
  DEL PEAK  6(2Q32.1) WILD-TYPE        73        26         83         62
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  6(2Q32.1) MUTATED            9        5         0
  DEL PEAK  6(2Q32.1) WILD-TYPE         39       46         4
D45V3, multiclass
            clus
vv           DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             1                            18
  STAGE IB                             9                            39
  STAGE II                             3                            29
  STAGE IIA                           11                            66
  STAGE IIB                           11                            73
  STAGE III                            3                            26
  STAGE IIIA                          14                            83
  STAGE IIIB                          10                            62
  STAGE IIIC                           9                            39
  STAGE IV                             5                            46
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  6(2Q32.1) MUTATED       4  16  41  19
  DEL PEAK  6(2Q32.1) WILD-TYPE    49 110 239 105
D45V4, multiclass
       clus
vv      DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  T0+T1                           4                            49
  T2                             16                           110
  T3                             41                           239
  T4                             19                           105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(2Q32.1) MUTATED    32  18  12  18
  DEL PEAK  6(2Q32.1) WILD-TYPE 168 164  84  79
D45V5, multiclass
    clus
vv   DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  N0                          32                           168
  N1                          18                           164
  N2                          12                            84
  N3                          18                            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"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    74   3
  DEL PEAK  6(2Q32.1) WILD-TYPE 439  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     74    3
  DEL PEAK  6(2Q32.1) WILD-TYPE  439   36
   clus
vv  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  0                          74                           439
  1                           3                            36
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    26  58
  DEL PEAK  6(2Q32.1) WILD-TYPE 156 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     26   58
  DEL PEAK  6(2Q32.1) WILD-TYPE  156  369
        clus
vv       DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  FEMALE                          26                           156
  MALE                            58                           369
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  6(2Q32.1) MUTATED                                       8
  DEL PEAK  6(2Q32.1) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q32.1) MUTATED                                                       22
  DEL PEAK  6(2Q32.1) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(2Q32.1) MUTATED                                                                   8
  DEL PEAK  6(2Q32.1) WILD-TYPE                                                                73
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  6(2Q32.1) MUTATED                                                 15
  DEL PEAK  6(2Q32.1) WILD-TYPE                                               63
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  6(2Q32.1) MUTATED                                                          5
  DEL PEAK  6(2Q32.1) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  6(2Q32.1) MUTATED                                                           0
  DEL PEAK  6(2Q32.1) WILD-TYPE                                                         8
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  6(2Q32.1) MUTATED                                          3
  DEL PEAK  6(2Q32.1) WILD-TYPE                                       10
D45V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  6(2Q32.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  6(2Q32.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            73
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             63
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED     1  83
  DEL PEAK  6(2Q32.1) WILD-TYPE   5 520
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED      1   83
  DEL PEAK  6(2Q32.1) WILD-TYPE    5  520
     clus
vv    DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  NO                            1                             5
  YES                          83                           520
[1] 2 2
[1] FALSE
D45V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q32.1) MUTATED    50   3   4   3
  DEL PEAK  6(2Q32.1) WILD-TYPE 297  15  15  22
D45V11, multiclass
    clus
vv   DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  R0                          50                           297
  R1                           3                            15
  R2                           4                            15
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(2Q32.1) MUTATED      18                         2
  DEL PEAK  6(2Q32.1) WILD-TYPE   111                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q32.1) MUTATED                                           0    55
  DEL PEAK  6(2Q32.1) WILD-TYPE                                         1   330
D45V13, multiclass
                                           clus
vv                                          DEL PEAK  6(2Q32.1) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              55
                                           clus
vv                                          DEL PEAK  6(2Q32.1) WILD-TYPE
  ASIAN                                                               111
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED     0  54
  DEL PEAK  6(2Q32.1) WILD-TYPE   7 340
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED      0   54
  DEL PEAK  6(2Q32.1) WILD-TYPE    7  340
                        clus
vv                       DEL PEAK  6(2Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  6(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           340
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK  7(2Q33.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q33.3) MUTATED    46  30
  DEL PEAK  7(2Q33.3) WILD-TYPE 308 191
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           76                           499 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           30                           191 
$`DEL PEAK  7(2Q33.3) MUTATED`
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 
       20.09         0.85         2.63        20.12        18.64         0.79 
TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 
       68.02        25.22         0.30        58.59         6.94         3.02 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A4MQ 
       16.47        13.55         5.49         5.92         0.10        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A8W8 TCGA-R6-A8WC 
       10.52        12.23        13.18         8.02         2.89         1.45 
TCGA-S8-A6BV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-Z6-AAPN 
       20.02        18.81        19.96        12.43        42.87         2.66 
TCGA-ZR-A9CJ TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7901 TCGA-BR-8058 
       19.73        19.33         9.17        12.16         3.45        17.49 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8369 TCGA-BR-8687 TCGA-CD-8525 TCGA-CD-8526 
        9.60        12.95        14.04         8.22         0.07         0.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4462 TCGA-CG-5720 TCGA-CG-5724 
        0.13         3.42        20.02         0.00         0.99        12.03 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-8576 
       12.66        11.93        17.19        15.22        19.50        14.66 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU 
       26.47         5.92        11.84        22.75        25.81         6.25 
TCGA-HU-A4H0 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-AB1V TCGA-VQ-A8DU 
        2.10        27.42        18.38         1.41         7.82         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PY 
       13.25        13.02        46.26        17.85        27.35        14.33 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J 
       22.09        40.08        32.94        21.11 

$`DEL PEAK  7(2Q33.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       13.94         8.94        16.24         4.21        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        6.21        33.27        20.78         3.88         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28         3.16        30.25         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
       24.00         3.68         4.70        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
       47.93        18.35         3.32         7.17         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        4.90        29.00         7.13         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        13.48        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       11.54        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03         0.13        33.11         5.16         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        9.30        15.78        12.69         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        3.42         4.80        15.35         9.27         4.44        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42         2.10        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       28.73        12.43         9.07        12.76        18.71        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        12.26        20.55         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        9.86        15.68        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        22.26         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
       13.18         0.30         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-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-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-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        1.02         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.36        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        10.26        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8578 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-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-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        0.23        18.08         1.51        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         0.10         6.51        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 
       16.87        19.04         5.79         0.92        48.79        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        64.57        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        16.14        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                       12.805                        12.760 
[1] "0.0 - 68.0 (12.8)"  "0.1 - 122.3 (12.8)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(2Q33.3) MUTATED         2        2        7        2        11
  DEL PEAK  7(2Q33.3) WILD-TYPE       9       17       41       30        66
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(2Q33.3) MUTATED          11         5         16         10
  DEL PEAK  7(2Q33.3) WILD-TYPE        73        24         81         62
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(2Q33.3) MUTATED            8        4         0
  DEL PEAK  7(2Q33.3) WILD-TYPE         40       47         4
D46V3, multiclass
            clus
vv           DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             2                            17
  STAGE IB                             7                            41
  STAGE II                             2                            30
  STAGE IIA                           11                            66
  STAGE IIB                           11                            73
  STAGE III                            5                            24
  STAGE IIIA                          16                            81
  STAGE IIIB                          10                            62
  STAGE IIIC                           8                            40
  STAGE IV                             4                            47
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  7(2Q33.3) MUTATED       4  12  47  15
  DEL PEAK  7(2Q33.3) WILD-TYPE    49 114 233 109
D46V4, multiclass
       clus
vv      DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  T0+T1                           4                            49
  T2                             12                           114
  T3                             47                           233
  T4                             15                           109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  7(2Q33.3) MUTATED    29  23  11  15
  DEL PEAK  7(2Q33.3) WILD-TYPE 171 159  85  82
D46V5, multiclass
    clus
vv   DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  N0                          29                           171
  N1                          23                           159
  N2                          11                            85
  N3                          15                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED    70   3
  DEL PEAK  7(2Q33.3) WILD-TYPE 443  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED     70    3
  DEL PEAK  7(2Q33.3) WILD-TYPE  443   36
   clus
vv  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  0                          70                           443
  1                           3                            36
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED    23  58
  DEL PEAK  7(2Q33.3) WILD-TYPE 159 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED     23   58
  DEL PEAK  7(2Q33.3) WILD-TYPE  159  369
        clus
vv       DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  FEMALE                          23                           159
  MALE                            58                           369
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  7(2Q33.3) MUTATED                                       7
  DEL PEAK  7(2Q33.3) WILD-TYPE                                    64
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q33.3) MUTATED                                                       16
  DEL PEAK  7(2Q33.3) WILD-TYPE                                                    146
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(2Q33.3) MUTATED                                                                   5
  DEL PEAK  7(2Q33.3) WILD-TYPE                                                                76
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  7(2Q33.3) MUTATED                                                 13
  DEL PEAK  7(2Q33.3) WILD-TYPE                                               65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  7(2Q33.3) MUTATED                                                          4
  DEL PEAK  7(2Q33.3) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  7(2Q33.3) MUTATED                                                           0
  DEL PEAK  7(2Q33.3) WILD-TYPE                                                         8
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  7(2Q33.3) MUTATED                                          4
  DEL PEAK  7(2Q33.3) WILD-TYPE                                        9
D46V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  7(2Q33.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK  7(2Q33.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED     2  79
  DEL PEAK  7(2Q33.3) WILD-TYPE   4 524
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED      2   79
  DEL PEAK  7(2Q33.3) WILD-TYPE    4  524
     clus
vv    DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  NO                            2                             4
  YES                          79                           524
[1] 2 2
[1] FALSE
D46V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(2Q33.3) MUTATED    40   4   3   0
  DEL PEAK  7(2Q33.3) WILD-TYPE 307  14  16  25
D46V11, multiclass
    clus
vv   DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  R0                          40                           307
  R1                           4                            14
  R2                           3                            16
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(2Q33.3) MUTATED      21                         2
  DEL PEAK  7(2Q33.3) WILD-TYPE   108                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(2Q33.3) MUTATED                                           0    50
  DEL PEAK  7(2Q33.3) WILD-TYPE                                         1   335
D46V13, multiclass
                                           clus
vv                                          DEL PEAK  7(2Q33.3) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              50
                                           clus
vv                                          DEL PEAK  7(2Q33.3) WILD-TYPE
  ASIAN                                                               108
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED     0  50
  DEL PEAK  7(2Q33.3) WILD-TYPE   7 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED      0   50
  DEL PEAK  7(2Q33.3) WILD-TYPE    7  344
                        clus
vv                       DEL PEAK  7(2Q33.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK  7(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK  8(2Q37.2) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(2Q37.2) MUTATED    71  43
  DEL PEAK  8(2Q37.2) WILD-TYPE 283 178
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          114                           461 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                           43                           178 
$`DEL PEAK  8(2Q37.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
       25.78        13.94        20.09         0.85         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FD TCGA-L5-A43H TCGA-L5-A4OR 
       18.64         0.79        14.50        68.02         0.30         3.16 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       58.59         6.94         3.02        16.47        13.55        13.22 
TCGA-L5-A8NT TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W 
       27.12         5.92        10.45        12.66         0.10        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
       12.59        12.59        12.33        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV 
       13.18         1.45         7.00        20.02        20.38        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-A8EZ 
        4.44        18.81        19.96        12.43        28.11        18.18 
TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-6565 TCGA-BR-6709 
       42.87         3.42         2.66        19.73         9.17        12.16 
TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 
       35.24         3.45        17.49        14.43        11.44         9.60 
TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8485 
       12.95        19.50        14.79         0.26        25.18         9.21 
TCGA-BR-8677 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8526 
        0.49         8.22        20.65        13.15         0.07         0.07 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4437 
        0.13         0.13         3.42        11.31        20.02         8.05 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-5578 
       14.01        19.07        18.97        12.00         1.02        12.66 
TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8576 
       20.55        17.19        15.22        15.98        10.55        14.66 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GP 
       11.24         2.96        26.47         5.92        22.75         8.98 
TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-AB1V TCGA-R5-A7ZE 
       12.95        27.42         1.41         6.74         7.82        18.21 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       13.25        13.02        22.19        27.35        64.57        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 
       18.74        20.81        22.68         9.04         4.54         5.72 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
       22.09        18.41        40.08        32.94        54.12        16.14 

$`DEL PEAK  8(2Q37.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       16.24         4.21        32.45         7.69         6.21        33.27 
TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         3.88         9.30         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96        14.86         4.67        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       44.75        60.39         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        3.16        30.25         4.31         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17         1.38         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.95        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        13.41        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       52.57        46.09        10.36        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.33        25.25        12.00         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ 
       12.69         5.29         3.42         4.80         9.27        22.82 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55        18.31         8.12        30.71        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-B7-5816 
       11.24         9.17        15.91        10.16         2.10        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       12.76        18.71         0.69        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         5.39        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 
       15.81         9.34        13.45         6.28         7.53        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         9.86        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
       13.18         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 
        0.13         0.16         0.10         0.10         0.10         9.34 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
        4.01        29.98        47.05        12.03        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        22.98        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        11.93        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 
       18.61        17.85        13.35        10.26        12.79        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         5.52         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-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-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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        5.19        13.08         6.44        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        1.81        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       19.04         5.79         0.92        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       35.24        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        26.24        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       61.22         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
       52.24         2.01        55.43         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        42.54        11.24        28.41        29.98        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        21.11        12.43        10.62         0.79 

  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                       13.165                        12.590 
[1] "0.1 - 68.0 (13.2)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(2Q37.2) MUTATED         2        4        9        7        15
  DEL PEAK  8(2Q37.2) WILD-TYPE       9       15       39       25        62
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(2Q37.2) MUTATED          18        10         19         14
  DEL PEAK  8(2Q37.2) WILD-TYPE        66        19         78         58
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(2Q37.2) MUTATED           10        7         1
  DEL PEAK  8(2Q37.2) WILD-TYPE         38       44         3
D47V3, multiclass
            clus
vv           DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             4                            15
  STAGE IB                             9                            39
  STAGE II                             7                            25
  STAGE IIA                           15                            62
  STAGE IIB                           18                            66
  STAGE III                           10                            19
  STAGE IIIA                          19                            78
  STAGE IIIB                          14                            58
  STAGE IIIC                          10                            38
  STAGE IV                             7                            44
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  8(2Q37.2) MUTATED       9  23  60  24
  DEL PEAK  8(2Q37.2) WILD-TYPE    44 103 220 100
D47V4, multiclass
       clus
vv      DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  T0+T1                           9                            44
  T2                             23                           103
  T3                             60                           220
  T4                             24                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(2Q37.2) MUTATED    43  37  16  19
  DEL PEAK  8(2Q37.2) WILD-TYPE 157 145  80  78
D47V5, multiclass
    clus
vv   DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  N0                          43                           157
  N1                          37                           145
  N2                          16                            80
  N3                          19                            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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED   105   3
  DEL PEAK  8(2Q37.2) WILD-TYPE 408  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED    105    3
  DEL PEAK  8(2Q37.2) WILD-TYPE  408   36
   clus
vv  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  0                         105                           408
  1                           3                            36
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED    37  81
  DEL PEAK  8(2Q37.2) WILD-TYPE 145 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED     37   81
  DEL PEAK  8(2Q37.2) WILD-TYPE  145  346
        clus
vv       DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  FEMALE                          37                           145
  MALE                            81                           346
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  8(2Q37.2) MUTATED                                       6
  DEL PEAK  8(2Q37.2) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(2Q37.2) MUTATED                                                       22
  DEL PEAK  8(2Q37.2) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(2Q37.2) MUTATED                                                                  16
  DEL PEAK  8(2Q37.2) WILD-TYPE                                                                65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  8(2Q37.2) MUTATED                                                 19
  DEL PEAK  8(2Q37.2) WILD-TYPE                                               59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  8(2Q37.2) MUTATED                                                          3
  DEL PEAK  8(2Q37.2) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  8(2Q37.2) MUTATED                                                           2
  DEL PEAK  8(2Q37.2) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  8(2Q37.2) MUTATED                                          3
  DEL PEAK  8(2Q37.2) WILD-TYPE                                       10
D47V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  8(2Q37.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  8(2Q37.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED     2 116
  DEL PEAK  8(2Q37.2) WILD-TYPE   4 487
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED      2  116
  DEL PEAK  8(2Q37.2) WILD-TYPE    4  487
     clus
vv    DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  NO                            2                             4
  YES                         116                           487
[1] 2 2
[1] FALSE
D47V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(2Q37.2) MUTATED    65   2   2   0
  DEL PEAK  8(2Q37.2) WILD-TYPE 282  16  17  25
D47V11, multiclass
    clus
vv   DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  R0                          65                           282
  R1                           2                            16
  R2                           2                            17
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(2Q37.2) MUTATED      28                         3
  DEL PEAK  8(2Q37.2) WILD-TYPE   101                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(2Q37.2) MUTATED                                           0    69
  DEL PEAK  8(2Q37.2) WILD-TYPE                                         1   316
D47V13, multiclass
                                           clus
vv                                          DEL PEAK  8(2Q37.2) MUTATED
  ASIAN                                                              28
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              69
                                           clus
vv                                          DEL PEAK  8(2Q37.2) WILD-TYPE
  ASIAN                                                               101
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED     0  71
  DEL PEAK  8(2Q37.2) WILD-TYPE   7 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED      0   71
  DEL PEAK  8(2Q37.2) WILD-TYPE    7  323
                        clus
vv                       DEL PEAK  8(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK  8(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           323
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK  9(3P26.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P26.2) MUTATED   142  85
  DEL PEAK  9(3P26.2) WILD-TYPE 212 136
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          227                           348 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                           85                           136 
$`DEL PEAK  9(3P26.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12         3.88         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FB TCGA-JY-A6FD TCGA-L5-A43E 
        9.96        14.50        12.16        60.39        68.02        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        0.30         4.31         8.94         4.70        32.61        47.93 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
        3.32         7.17         3.16        58.59         4.90         7.13 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         7.40        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV TCGA-LN-A49K 
       12.92        16.47        13.55         5.49        52.57         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       15.52        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       10.52        12.00        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.82         7.59         7.04        29.59         2.89        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
        7.00        20.02        20.38         3.42         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        12.43        18.31         8.12        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       10.16         3.42         2.10        11.01         9.44         6.61 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7704 
       18.35        19.33         9.17        25.61        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         9.07        18.71        17.49         0.69 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8484 
        2.66        16.31         7.40        13.08         5.39        25.18 
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         8.22 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68         7.53        22.26         1.48        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         9.34 
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-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5730 
       47.05        12.03        18.97        36.00        15.02         4.01 
TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 
       12.66        18.54        13.35        17.19        15.22        12.79 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
       11.31         9.76        15.65         0.62         7.99        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 
       14.07        17.06         0.56         5.52        12.59        14.17 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
       12.30         3.25        22.75         6.25         2.10        23.84 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       12.30        21.21        18.38         1.41         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        6.51         5.56         5.56        60.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW 
       45.67        18.21         8.52         8.61        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
      115.69         8.94         5.79         0.92         5.46        13.25 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU 
        7.73        22.19        12.79         2.70        17.85        27.35 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
       14.33        36.69        36.16         9.50         9.73         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A 
        4.54        21.04        42.54        22.09        18.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       29.98        54.12        21.11        12.43         0.79 

$`DEL PEAK  9(3P26.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IC-A6RF 
       25.78        31.27        58.55         7.63        32.45         6.21 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 
       18.64         9.30        12.82        14.86         4.67       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.00         3.68        19.99        21.01        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A891 
       29.00         7.43         8.71        25.12         0.36         3.95 
TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
        3.02        13.48        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L 
       13.41        27.12        83.24        46.09        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A9 TCGA-LN-A7HY 
       12.66         0.10        13.25        12.59        11.54        12.03 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.16         8.02         5.06        14.70         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        9.30        15.78         1.45         5.29         4.80        15.35 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        4.44        22.82         1.55        28.11         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         3.45        12.76 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        0.56        12.95         2.20        15.58         6.18        19.50 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       15.85         3.72         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       13.45         6.28         7.53         0.49        16.44         9.86 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56        13.87         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-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         3.42        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        6.58        12.20         0.10        12.62        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
        1.02        14.01        29.98        19.07        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-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-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.36        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        10.26        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        13.71        11.24        11.44         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.40         7.13        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27        11.38         3.48        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30         5.59        11.84        24.20        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        12.95        19.36         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42         3.45        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       13.08         6.74         1.81         7.82        13.51         2.53 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       20.15         3.72        19.73        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        9.24        11.05         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT 
       71.38        57.44        35.61        16.87        19.04        48.79 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        65.16        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81        22.68         1.71         7.36        52.24         9.04 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T 
       55.43         6.58         5.72        64.18         2.66        11.24 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       40.08        28.41        17.13        26.04        16.14        10.62 

  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                        12.59                         12.95 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P26.2) MUTATED         5        7       17        8        34
  DEL PEAK  9(3P26.2) WILD-TYPE       6       12       31       24        43
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P26.2) MUTATED          33        15         42         25
  DEL PEAK  9(3P26.2) WILD-TYPE        51        14         55         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(3P26.2) MUTATED           17       19         2
  DEL PEAK  9(3P26.2) WILD-TYPE         31       32         2
D48V3, multiclass
            clus
vv           DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  STAGE I                              5                             6
  STAGE IA                             7                            12
  STAGE IB                            17                            31
  STAGE II                             8                            24
  STAGE IIA                           34                            43
  STAGE IIB                           33                            51
  STAGE III                           15                            14
  STAGE IIIA                          42                            55
  STAGE IIIB                          25                            47
  STAGE IIIC                          17                            31
  STAGE IV                            19                            32
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  9(3P26.2) MUTATED      24  44 115  44
  DEL PEAK  9(3P26.2) WILD-TYPE    29  82 165  80
D48V4, multiclass
       clus
vv      DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  T0+T1                          24                            29
  T2                             44                            82
  T3                            115                           165
  T4                             44                            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  9(3P26.2) MUTATED    76  75  42  31
  DEL PEAK  9(3P26.2) WILD-TYPE 124 107  54  66
D48V5, multiclass
    clus
vv   DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  N0                          76                           124
  N1                          75                           107
  N2                          42                            54
  N3                          31                            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"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED   195  18
  DEL PEAK  9(3P26.2) WILD-TYPE 318  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED    195   18
  DEL PEAK  9(3P26.2) WILD-TYPE  318   21
   clus
vv  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  0                         195                           318
  1                          18                            21
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED    61 176
  DEL PEAK  9(3P26.2) WILD-TYPE 121 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED     61  176
  DEL PEAK  9(3P26.2) WILD-TYPE  121  251
        clus
vv       DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  FEMALE                          61                           121
  MALE                           176                           251
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK  9(3P26.2) MUTATED                                      15
  DEL PEAK  9(3P26.2) WILD-TYPE                                    56
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P26.2) MUTATED                                                       48
  DEL PEAK  9(3P26.2) WILD-TYPE                                                    114
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P26.2) MUTATED                                                                  35
  DEL PEAK  9(3P26.2) WILD-TYPE                                                                46
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK  9(3P26.2) MUTATED                                                 27
  DEL PEAK  9(3P26.2) WILD-TYPE                                               51
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK  9(3P26.2) MUTATED                                                          5
  DEL PEAK  9(3P26.2) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK  9(3P26.2) MUTATED                                                           3
  DEL PEAK  9(3P26.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK  9(3P26.2) MUTATED                                          3
  DEL PEAK  9(3P26.2) WILD-TYPE                                       10
D48V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK  9(3P26.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK  9(3P26.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            46
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED     2 235
  DEL PEAK  9(3P26.2) WILD-TYPE   4 368
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED      2  235
  DEL PEAK  9(3P26.2) WILD-TYPE    4  368
     clus
vv    DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  NO                            2                             4
  YES                         235                           368
[1] 2 2
[1] FALSE
D48V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P26.2) MUTATED   109   5   8   6
  DEL PEAK  9(3P26.2) WILD-TYPE 238  13  11  19
D48V11, multiclass
    clus
vv   DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  R0                         109                           238
  R1                           5                            13
  R2                           8                            11
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(3P26.2) MUTATED      55                         4
  DEL PEAK  9(3P26.2) WILD-TYPE    74                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(3P26.2) MUTATED                                           1   148
  DEL PEAK  9(3P26.2) WILD-TYPE                                         0   237
D48V13, multiclass
                                           clus
vv                                          DEL PEAK  9(3P26.2) MUTATED
  ASIAN                                                              55
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             148
                                           clus
vv                                          DEL PEAK  9(3P26.2) WILD-TYPE
  ASIAN                                                                74
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED     2 147
  DEL PEAK  9(3P26.2) WILD-TYPE   5 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED      2  147
  DEL PEAK  9(3P26.2) WILD-TYPE    5  247
                        clus
vv                       DEL PEAK  9(3P26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       DEL PEAK  9(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           247
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 10(3P14.2) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3P14.2) MUTATED   158 103
  DEL PEAK 10(3P14.2) WILD-TYPE 196 118
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          261                           314 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          103                           118 
$`DEL PEAK 10(3P14.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        20.09         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        23.41         9.96        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       68.02        30.25         0.30         4.31         8.94        24.00 
TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
        3.68         4.70        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        7.17         1.38         7.13         7.43         6.94         2.60 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        0.36         7.40         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49K 
       13.55         5.49         8.71        13.41        52.57         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        22.39         0.10        15.52        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.03        13.18         0.13        33.11         5.16         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        7.59         7.04         2.89        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         3.42         4.80         9.27        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI 
       10.16         3.42         2.10         2.66        26.70        19.56 
TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
       11.01         6.61        17.29        19.33         9.17        25.61 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       31.20        32.94        35.24        15.42        28.01        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        3.45         9.07        18.71        17.49        11.44         0.69 
TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 
        2.66         5.39        25.18         9.21        20.22        15.68 
TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        8.22        13.87         7.53        22.26         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.53        13.51        20.65         1.15        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-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 
        0.13         9.34        20.02         3.02        15.95         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-4466 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       18.97        36.00         1.02        12.03        15.02         4.01 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.36        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A4YY 
       10.26        15.22        12.79        12.33        14.27        13.78 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31        11.44         9.76         7.40         0.62         7.99 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       19.53        14.07        17.06         0.56         5.52        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G6 
        5.92        12.59        14.17        11.41        12.10        12.30 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-A6RI 
        6.25         2.10        23.84         8.88        21.21        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        5.56        13.51         5.56        60.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8MW 
       45.67        18.21         8.52        61.25        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P5 
        8.94         5.79         5.46        13.25        34.45         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY 
       22.19         2.70        17.85         9.27        13.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       18.74        36.16         9.50         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
        4.54        22.09        18.41        32.94        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       26.04        12.43         0.79 

$`DEL PEAK 10(3P14.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IC-A6RF TCGA-IG-A4QT 
       25.78        31.27        58.55         7.63         6.21         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE 
       12.82        14.86         4.67       122.10        60.39         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       41.52        42.77        25.41        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OI TCGA-L5-A4ON 
       25.22        24.03         6.28         3.16        19.99        18.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W 
        3.16        58.59         4.90        29.00         8.71        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM 
        3.95         3.02        55.50        13.48        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49R 
       21.37        27.12        83.24        46.09        10.36         0.10 
TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.10        11.54         7.82         5.06        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB 
        6.35        53.95         9.30        15.78         1.45         5.29 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-ZR-A9CJ TCGA-B7-5818 
       15.35         4.44        22.82         1.55        19.73        11.70 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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 
       13.87        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 
       19.89        12.16         8.98        21.11        30.90        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 
        9.21        24.76        23.93        18.15        28.73        12.43 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       12.76        14.43        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 
       19.17        14.79         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         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        0.49        11.54        15.81        16.44         9.86        10.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       12.56         6.08        13.41        13.51         8.98        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-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        3.42        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 
        0.10        12.62        27.02         1.02        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10        69.04        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 
       12.66        11.93        19.13        18.61        17.85        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       15.16        14.76        13.71        11.24         2.96        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27        11.38         3.48        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8608 
       13.58         0.23        18.08         1.51        14.27        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76        24.30         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         6.51        10.19         0.26        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       12.30         9.67         8.81        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        3.39         5.36        13.08         1.81         7.82         2.53 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       20.15         3.72        19.73         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         5.13       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.02        18.48        35.24        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         1.87        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       61.22        20.81        22.68         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       52.24         6.58         5.72        64.18        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6I 
       42.54        11.24        40.08        28.41        17.13        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11        10.62 

  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                        12.43                         13.08 
[1] "0.1 - 68.0 (12.4)"  "0.0 - 122.3 (13.1)"
[1] "hr=" "1.3"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3P14.2) MUTATED         5        7       17       13        44
  DEL PEAK 10(3P14.2) WILD-TYPE       6       12       31       19        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3P14.2) MUTATED          41        17         49         25
  DEL PEAK 10(3P14.2) WILD-TYPE        43        12         48         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(3P14.2) MUTATED           16       21         3
  DEL PEAK 10(3P14.2) WILD-TYPE         32       30         1
D49V3, multiclass
            clus
vv           DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  STAGE I                              5                             6
  STAGE IA                             7                            12
  STAGE IB                            17                            31
  STAGE II                            13                            19
  STAGE IIA                           44                            33
  STAGE IIB                           41                            43
  STAGE III                           17                            12
  STAGE IIIA                          49                            48
  STAGE IIIB                          25                            47
  STAGE IIIC                          16                            32
  STAGE IV                            21                            30
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 10(3P14.2) MUTATED      29  56 131  45
  DEL PEAK 10(3P14.2) WILD-TYPE    24  70 149  79
D49V4, multiclass
       clus
vv      DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  T0+T1                          29                            24
  T2                             56                            70
  T3                            131                           149
  T4                             45                            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 10(3P14.2) MUTATED    93  90  44  32
  DEL PEAK 10(3P14.2) WILD-TYPE 107  92  52  65
D49V5, multiclass
    clus
vv   DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  N0                          93                           107
  N1                          90                            92
  N2                          44                            52
  N3                          32                            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"
D49V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED   221  21
  DEL PEAK 10(3P14.2) WILD-TYPE 292  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED    221   21
  DEL PEAK 10(3P14.2) WILD-TYPE  292   18
   clus
vv  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  0                         221                           292
  1                          21                            18
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED    76 193
  DEL PEAK 10(3P14.2) WILD-TYPE 106 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED     76  193
  DEL PEAK 10(3P14.2) WILD-TYPE  106  234
        clus
vv       DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  FEMALE                          76                           106
  MALE                           193                           234
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 10(3P14.2) MUTATED                                      19
  DEL PEAK 10(3P14.2) WILD-TYPE                                    52
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3P14.2) MUTATED                                                       51
  DEL PEAK 10(3P14.2) WILD-TYPE                                                    111
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3P14.2) MUTATED                                                                  36
  DEL PEAK 10(3P14.2) WILD-TYPE                                                                45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 10(3P14.2) MUTATED                                                 36
  DEL PEAK 10(3P14.2) WILD-TYPE                                               42
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 10(3P14.2) MUTATED                                                          4
  DEL PEAK 10(3P14.2) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 10(3P14.2) MUTATED                                                           4
  DEL PEAK 10(3P14.2) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 10(3P14.2) MUTATED                                          5
  DEL PEAK 10(3P14.2) WILD-TYPE                                        8
D49V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 10(3P14.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  DEL PEAK 10(3P14.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      111
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED     2 267
  DEL PEAK 10(3P14.2) WILD-TYPE   4 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED      2  267
  DEL PEAK 10(3P14.2) WILD-TYPE    4  336
     clus
vv    DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  NO                            2                             4
  YES                         267                           336
[1] 2 2
[1] FALSE
D49V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(3P14.2) MUTATED   134   3   7   3
  DEL PEAK 10(3P14.2) WILD-TYPE 213  15  12  22
D49V11, multiclass
    clus
vv   DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  R0                         134                           213
  R1                           3                            15
  R2                           7                            12
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(3P14.2) MUTATED      68                         2
  DEL PEAK 10(3P14.2) WILD-TYPE    61                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(3P14.2) MUTATED                                           0   160
  DEL PEAK 10(3P14.2) WILD-TYPE                                         1   225
D49V13, multiclass
                                           clus
vv                                          DEL PEAK 10(3P14.2) MUTATED
  ASIAN                                                              68
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             160
                                           clus
vv                                          DEL PEAK 10(3P14.2) WILD-TYPE
  ASIAN                                                                61
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED     3 168
  DEL PEAK 10(3P14.2) WILD-TYPE   4 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED      3  168
  DEL PEAK 10(3P14.2) WILD-TYPE    4  226
                        clus
vv                       DEL PEAK 10(3P14.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         168
                        clus
vv                       DEL PEAK 10(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           226
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 11(3Q11.1) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(3Q11.1) MUTATED    56  37
  DEL PEAK 11(3Q11.1) WILD-TYPE 298 184
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           93                           482 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           37                           184 
$`DEL PEAK 11(3Q11.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YB 
       14.30        13.94         4.21        32.45         7.69         2.63 
TCGA-IG-A3YC TCGA-IG-A5S3 TCGA-JY-A6FD TCGA-JY-A938 TCGA-L5-A43E TCGA-L5-A43H 
       20.12        23.41        68.02        25.41        30.25         0.30 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A8NH TCGA-LN-A49L 
       32.61         3.32         7.43         0.36        12.92        10.45 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
        0.10        12.46         0.10         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASW 
       12.03        13.18         2.89        12.69         7.00         9.27 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 
       46.19        10.16        17.29        19.33         9.17        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
       15.42        28.01        18.71        11.44         0.69         2.66 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ 
        5.39         9.21        20.22        15.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        1.48        12.89         0.72        13.51         1.15        13.64 
TCGA-CD-5800 TCGA-CD-8533 TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 
       13.15         0.13        20.02        54.08        14.01        12.03 
TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-A6EX 
       18.97        12.03        12.66        20.55        15.22        11.31 
TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GC 
        0.62        17.06         0.56         5.52        14.17         3.25 
TCGA-HU-A4GU TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IP-7968 TCGA-KB-A6F5 
        6.25        21.21         5.19         1.41         2.53         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZF TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8P5 
       37.64         9.86         8.52         5.79        13.25         7.73 
TCGA-VQ-A8PJ TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R 
        2.70        18.74         9.50         9.73        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6D 
       22.09        29.98        17.13 

$`DEL PEAK 11(3Q11.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       18.64         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        60.39         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       21.70        23.18        31.56        25.22        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93        18.35         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.13         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       27.12        83.24        52.57        46.09        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.66        12.43        13.41        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25         0.10        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
       22.39        15.52        11.54        12.33        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.00         0.13        33.11         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BV 
        6.35        53.95         9.30        15.78         1.45        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       20.38         5.29         3.42         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       18.81        19.96        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        15.91         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76        17.49        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86         8.22        10.68        12.56        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
        0.66        19.36         0.46        20.65        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         0.07 
TCGA-CD-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-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.16         0.10         0.10         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05         4.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         0.00         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-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-D7-5579 
        4.01        69.04        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-D7-6526 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-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
        9.76         2.96        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         7.99        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       11.38         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-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        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         6.44         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        1.81         7.82        13.51        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        45.67        18.21        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87        19.04         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       22.19         2.50        12.79        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z 
       20.81        22.68         1.71        36.16         7.36        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       64.18         2.66        11.24        18.41        40.08        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                          0.1                           0.0 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                        12.23                         12.82 
[1] "0.1 - 68.0 (12.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(3Q11.1) MUTATED         2        2        4        5        11
  DEL PEAK 11(3Q11.1) WILD-TYPE       9       17       44       27        66
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(3Q11.1) MUTATED          17         5         19          9
  DEL PEAK 11(3Q11.1) WILD-TYPE        67        24         78         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(3Q11.1) MUTATED            6       10         0
  DEL PEAK 11(3Q11.1) WILD-TYPE         42       41         4
D50V3, multiclass
            clus
vv           DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             2                            17
  STAGE IB                             4                            44
  STAGE II                             5                            27
  STAGE IIA                           11                            66
  STAGE IIB                           17                            67
  STAGE III                            5                            24
  STAGE IIIA                          19                            78
  STAGE IIIB                           9                            63
  STAGE IIIC                           6                            42
  STAGE IV                            10                            41
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 11(3Q11.1) MUTATED      11  14  43  24
  DEL PEAK 11(3Q11.1) WILD-TYPE    42 112 237 100
D50V4, multiclass
       clus
vv      DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  T0+T1                          11                            42
  T2                             14                           112
  T3                             43                           237
  T4                             24                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 11(3Q11.1) MUTATED    29  33  19  11
  DEL PEAK 11(3Q11.1) WILD-TYPE 171 149  77  86
D50V5, multiclass
    clus
vv   DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  N0                          29                           171
  N1                          33                           149
  N2                          19                            77
  N3                          11                            86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED    81   7
  DEL PEAK 11(3Q11.1) WILD-TYPE 432  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED     81    7
  DEL PEAK 11(3Q11.1) WILD-TYPE  432   32
   clus
vv  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  0                          81                           432
  1                           7                            32
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED    25  71
  DEL PEAK 11(3Q11.1) WILD-TYPE 157 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED     25   71
  DEL PEAK 11(3Q11.1) WILD-TYPE  157  356
        clus
vv       DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  FEMALE                          25                           157
  MALE                            71                           356
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 11(3Q11.1) MUTATED                                       5
  DEL PEAK 11(3Q11.1) WILD-TYPE                                    66
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(3Q11.1) MUTATED                                                       27
  DEL PEAK 11(3Q11.1) WILD-TYPE                                                    135
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(3Q11.1) MUTATED                                                                  15
  DEL PEAK 11(3Q11.1) WILD-TYPE                                                                66
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 11(3Q11.1) MUTATED                                                 11
  DEL PEAK 11(3Q11.1) WILD-TYPE                                               67
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 11(3Q11.1) MUTATED                                                          3
  DEL PEAK 11(3Q11.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 11(3Q11.1) MUTATED                                                           1
  DEL PEAK 11(3Q11.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 11(3Q11.1) MUTATED                                          2
  DEL PEAK 11(3Q11.1) WILD-TYPE                                       11
D50V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 11(3Q11.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 11(3Q11.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED     0  96
  DEL PEAK 11(3Q11.1) WILD-TYPE   6 507
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED      0   96
  DEL PEAK 11(3Q11.1) WILD-TYPE    6  507
     clus
vv    DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  NO                            0                             6
  YES                          96                           507
[1] 2 2
[1] FALSE
D50V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(3Q11.1) MUTATED    56   1   4   2
  DEL PEAK 11(3Q11.1) WILD-TYPE 291  17  15  23
D50V11, multiclass
    clus
vv   DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  R0                          56                           291
  R1                           1                            17
  R2                           4                            15
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(3Q11.1) MUTATED      21                         2
  DEL PEAK 11(3Q11.1) WILD-TYPE   108                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(3Q11.1) MUTATED                                           0    59
  DEL PEAK 11(3Q11.1) WILD-TYPE                                         1   326
D50V13, multiclass
                                           clus
vv                                          DEL PEAK 11(3Q11.1) MUTATED
  ASIAN                                                              21
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              59
                                           clus
vv                                          DEL PEAK 11(3Q11.1) WILD-TYPE
  ASIAN                                                               108
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED     1  62
  DEL PEAK 11(3Q11.1) WILD-TYPE   6 332
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED      1   62
  DEL PEAK 11(3Q11.1) WILD-TYPE    6  332
                        clus
vv                       DEL PEAK 11(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 11(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           332
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 12(3Q26.31) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(3Q26.31) MUTATED    33  25
  DEL PEAK 12(3Q26.31) WILD-TYPE 321 196
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            58                            517 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            25                            196 
$`DEL PEAK 12(3Q26.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IC-A6RE TCGA-JY-A938 TCGA-JY-A93D 
       25.78        14.30        13.94         7.69        25.41        31.56 
TCGA-L5-A4OH TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NW TCGA-R6-A6DN 
       32.61         7.43         3.95        12.92        46.09         8.02 
TCGA-RE-A7BO TCGA-VR-A8EU TCGA-X8-AAAR TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 
        7.00        18.31        10.16        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        13.87        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         9.34        54.08 
TCGA-CG-4441 TCGA-CG-4466 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-8573 TCGA-D7-A6EX 
       14.01        18.97        12.66        17.19        19.50        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF 
       11.44         2.96         7.99         5.52        14.17        25.81 
TCGA-HU-A4GU TCGA-IN-7806 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZF 
        6.25        21.21         5.56        37.64         9.86         8.52 
TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A91X 
       16.67         5.46        13.25        22.19        36.16         9.50 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA6B 
       21.04        42.54        22.09        29.98 

$`DEL PEAK 12(3Q26.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       14.86         4.67        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        6.94         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        35.97        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35         0.10        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         5.16         7.82         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         1.45        12.69        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       17.29        13.68        19.33        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         3.45         9.07        12.76        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         2.66        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        15.68         8.22        12.56         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       22.26         1.48        13.41        13.51         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        69.04        21.07         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        10.26        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ 
       15.16        13.78        14.76        13.71        11.24         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        46.26        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       17.85         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71         7.36         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       11.24        18.41        40.08        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                         54.08                         122.30 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                         13.69                          12.62 
[1] "0.1 - 54.1 (13.7)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(3Q26.31) MUTATED         1        1        6        2         4
  DEL PEAK 12(3Q26.31) WILD-TYPE      10       18       42       30        73
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(3Q26.31) MUTATED          12         2         12          8
  DEL PEAK 12(3Q26.31) WILD-TYPE        72        27         85         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(3Q26.31) MUTATED            4        5         0
  DEL PEAK 12(3Q26.31) WILD-TYPE         44       46         4
D51V3, multiclass
            clus
vv           DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              1                             18
  STAGE IB                              6                             42
  STAGE II                              2                             30
  STAGE IIA                             4                             73
  STAGE IIB                            12                             72
  STAGE III                             2                             27
  STAGE IIIA                           12                             85
  STAGE IIIB                            8                             64
  STAGE IIIC                            4                             44
  STAGE IV                              5                             46
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 12(3Q26.31) MUTATED       8   9  31  12
  DEL PEAK 12(3Q26.31) WILD-TYPE    45 117 249 112
D51V4, multiclass
       clus
vv      DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  T0+T1                            8                             45
  T2                               9                            117
  T3                              31                            249
  T4                              12                            112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 12(3Q26.31) MUTATED    17  19  14   9
  DEL PEAK 12(3Q26.31) WILD-TYPE 183 163  82  88
D51V5, multiclass
    clus
vv   DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  N0                           17                            183
  N1                           19                            163
  N2                           14                             82
  N3                            9                             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED    54   3
  DEL PEAK 12(3Q26.31) WILD-TYPE 459  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED     54    3
  DEL PEAK 12(3Q26.31) WILD-TYPE  459   36
   clus
vv  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  0                           54                            459
  1                            3                             36
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED    17  45
  DEL PEAK 12(3Q26.31) WILD-TYPE 165 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED     17   45
  DEL PEAK 12(3Q26.31) WILD-TYPE  165  382
        clus
vv       DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  FEMALE                           17                            165
  MALE                             45                            382
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 12(3Q26.31) MUTATED                                       4
  DEL PEAK 12(3Q26.31) WILD-TYPE                                    67
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(3Q26.31) MUTATED                                                       16
  DEL PEAK 12(3Q26.31) WILD-TYPE                                                    146
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(3Q26.31) MUTATED                                                                  13
  DEL PEAK 12(3Q26.31) WILD-TYPE                                                                68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 12(3Q26.31) MUTATED                                                 11
  DEL PEAK 12(3Q26.31) WILD-TYPE                                               67
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 12(3Q26.31) MUTATED                                                          1
  DEL PEAK 12(3Q26.31) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 12(3Q26.31) MUTATED                                                           0
  DEL PEAK 12(3Q26.31) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 12(3Q26.31) MUTATED                                          2
  DEL PEAK 12(3Q26.31) WILD-TYPE                                       11
D51V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 12(3Q26.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 12(3Q26.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         67
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED     1  61
  DEL PEAK 12(3Q26.31) WILD-TYPE   5 542
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED      1   61
  DEL PEAK 12(3Q26.31) WILD-TYPE    5  542
     clus
vv    DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  NO                             1                              5
  YES                           61                            542
[1] 2 2
[1] FALSE
D51V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 12(3Q26.31) MUTATED    42   1   0   2
  DEL PEAK 12(3Q26.31) WILD-TYPE 305  17  19  23
D51V11, multiclass
    clus
vv   DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  R0                           42                            305
  R1                            1                             17
  R2                            0                             19
  RX                            2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(3Q26.31) MUTATED       8                         2
  DEL PEAK 12(3Q26.31) WILD-TYPE   121                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 12(3Q26.31) MUTATED                                           0
  DEL PEAK 12(3Q26.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 12(3Q26.31) MUTATED      43
  DEL PEAK 12(3Q26.31) WILD-TYPE   342
D51V13, multiclass
                                           clus
vv                                          DEL PEAK 12(3Q26.31) MUTATED
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               43
                                           clus
vv                                          DEL PEAK 12(3Q26.31) WILD-TYPE
  ASIAN                                                                121
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED     0  36
  DEL PEAK 12(3Q26.31) WILD-TYPE   7 358
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED      0   36
  DEL PEAK 12(3Q26.31) WILD-TYPE    7  358
                        clus
vv                       DEL PEAK 12(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 12(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            358
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 13(4P16.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4P16.3) MUTATED   147 103
  DEL PEAK 13(4P16.3) WILD-TYPE 207 118
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          250                           325 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          103                           118 
$`DEL PEAK 13(4P16.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21         7.69        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 
       20.12        18.64         3.88         0.79         9.96         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93E 
       12.16        44.75        60.39         3.68        41.52        25.22 
TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OJ 
        3.16         8.94        24.00         3.68         4.70        21.01 
TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Y 
       47.93         3.16         4.90         7.13         7.43         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.40         3.95        35.97        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         5.49        13.41        27.12        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        12.43         0.10        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
        0.10        12.46        12.59        12.49        12.76         0.10 
TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       15.52        13.22        12.33        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ 
       13.18         0.13         8.02         5.06         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30         2.89         1.45        12.69         7.00        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        3.42         4.80         9.27         4.44        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4D 
       12.43         1.55        18.31         8.12        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-B7-A5TJ TCGA-B7-A5TN 
       15.06        11.24        15.91         3.42        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 
        6.61         7.43        18.35        17.29         9.17        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        18.15        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8286 
        3.45         9.07        18.71        17.49         9.60        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 
        2.66        16.31         2.20        15.58         7.40        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       17.52        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         9.86        15.68        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        22.26         1.48         0.72         0.66        13.51 
TCGA-BR-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         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       11.61        12.20        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        18.21        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         7.99        72.23 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 
       11.38        14.07        17.06         5.52        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        12.59        14.17        12.10        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO 
        9.67        27.42        21.21        18.81         5.36         1.41 
TCGA-IN-A6RP TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A663 
        6.44         2.53         5.56        60.56         3.72         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
       45.67        18.21         6.08         9.24        11.05        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU 
       37.91       115.69         8.94        35.61         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 
       13.25        18.48        35.24        21.73        34.45        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
        7.73        46.26        22.19        12.79         2.70         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       27.35        65.16        36.69        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
       52.24         9.04         4.54        21.04        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       22.09        32.94        29.98        54.12 

$`DEL PEAK 13(4P16.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3YB 
       25.78        31.27         7.63        32.45         6.21         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        9.30         0.53        17.03        23.41        12.82        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       14.50       122.10        68.02        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        4.31        32.61        19.99        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38        58.59        29.00         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM 
       25.12         3.02        55.50         2.66        13.48         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49S 
       21.37         8.71        83.24        10.36        13.41        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        13.25        12.59        22.39        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
        4.47        25.25        10.52        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-S8-A6BV 
        7.59        14.70        29.59        53.95        15.78        20.02 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        5.29        15.35        18.81        28.11        30.71        18.18 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
        9.17        10.16         2.10         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 
       11.70        19.56         9.47         6.97         4.64        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 
       32.94        12.82        35.24        23.93        15.32        12.43 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       12.76        14.43        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        8.05         0.56         6.18        19.50        13.08         0.26 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        13.45         6.28         7.53        15.81        16.44 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        8.22        12.56        13.87         6.08        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53        12.82        19.36 
TCGA-BR-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         3.42        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 
       14.01        29.98        21.99         0.00         9.01        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 
       15.98        12.79        10.55        12.33        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.24        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         0.62        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 
       13.58         0.56         0.23        18.08        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        10.19        19.36        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45         3.39        18.38         5.19        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       20.15        37.64        19.73         8.52        61.25         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ 
       57.44        16.87        19.04         0.92        48.79        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK 
       27.88        28.96        34.29        16.31         2.50        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       14.33        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       22.68         1.71         7.36         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        64.18         2.66        18.41        40.08        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        26.04        16.14        21.11        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                       12.215                        13.150 
[1] "0.1 - 115.7 (12.2)" "0.0 - 122.3 (13.2)"
[1] "hr=" "1.2"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4P16.3) MUTATED         4        6       17       14        39
  DEL PEAK 13(4P16.3) WILD-TYPE       7       13       31       18        38
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4P16.3) MUTATED          35        17         46         28
  DEL PEAK 13(4P16.3) WILD-TYPE        49        12         51         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(4P16.3) MUTATED           16       18         1
  DEL PEAK 13(4P16.3) WILD-TYPE         32       33         3
D52V3, multiclass
            clus
vv           DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  STAGE I                              4                             7
  STAGE IA                             6                            13
  STAGE IB                            17                            31
  STAGE II                            14                            18
  STAGE IIA                           39                            38
  STAGE IIB                           35                            49
  STAGE III                           17                            12
  STAGE IIIA                          46                            51
  STAGE IIIB                          28                            44
  STAGE IIIC                          16                            32
  STAGE IV                            18                            33
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 13(4P16.3) MUTATED      22  49 132  43
  DEL PEAK 13(4P16.3) WILD-TYPE    31  77 148  81
D52V4, multiclass
       clus
vv      DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  T0+T1                          22                            31
  T2                             49                            77
  T3                            132                           148
  T4                             43                            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 13(4P16.3) MUTATED    83  84  45  32
  DEL PEAK 13(4P16.3) WILD-TYPE 117  98  51  65
D52V5, multiclass
    clus
vv   DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  N0                          83                           117
  N1                          84                            98
  N2                          45                            51
  N3                          32                            65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED   226  12
  DEL PEAK 13(4P16.3) WILD-TYPE 287  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED    226   12
  DEL PEAK 13(4P16.3) WILD-TYPE  287   27
   clus
vv  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  0                         226                           287
  1                          12                            27
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED    65 198
  DEL PEAK 13(4P16.3) WILD-TYPE 117 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED     65  198
  DEL PEAK 13(4P16.3) WILD-TYPE  117  229
        clus
vv       DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  FEMALE                          65                           117
  MALE                           198                           229
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 13(4P16.3) MUTATED                                      23
  DEL PEAK 13(4P16.3) WILD-TYPE                                    48
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4P16.3) MUTATED                                                       57
  DEL PEAK 13(4P16.3) WILD-TYPE                                                    105
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4P16.3) MUTATED                                                                  31
  DEL PEAK 13(4P16.3) WILD-TYPE                                                                50
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 13(4P16.3) MUTATED                                                 39
  DEL PEAK 13(4P16.3) WILD-TYPE                                               39
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 13(4P16.3) MUTATED                                                          9
  DEL PEAK 13(4P16.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 13(4P16.3) MUTATED                                                           3
  DEL PEAK 13(4P16.3) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 13(4P16.3) MUTATED                                          6
  DEL PEAK 13(4P16.3) WILD-TYPE                                        7
D52V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 13(4P16.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    6
                                                                   clus
vv                                                                  DEL PEAK 13(4P16.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      105
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED     2 261
  DEL PEAK 13(4P16.3) WILD-TYPE   4 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      2  261
  DEL PEAK 13(4P16.3) WILD-TYPE    4  342
     clus
vv    DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  NO                            2                             4
  YES                         261                           342
[1] 2 2
[1] FALSE
D52V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4P16.3) MUTATED   135   7   4   9
  DEL PEAK 13(4P16.3) WILD-TYPE 212  11  15  16
D52V11, multiclass
    clus
vv   DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  R0                         135                           212
  R1                           7                            11
  R2                           4                            15
  RX                           9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(4P16.3) MUTATED      62                         5
  DEL PEAK 13(4P16.3) WILD-TYPE    67                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(4P16.3) MUTATED                                           0   166
  DEL PEAK 13(4P16.3) WILD-TYPE                                         1   219
D52V13, multiclass
                                           clus
vv                                          DEL PEAK 13(4P16.3) MUTATED
  ASIAN                                                              62
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             166
                                           clus
vv                                          DEL PEAK 13(4P16.3) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED     3 168
  DEL PEAK 13(4P16.3) WILD-TYPE   4 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      3  168
  DEL PEAK 13(4P16.3) WILD-TYPE    4  226
                        clus
vv                       DEL PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         168
                        clus
vv                       DEL PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           226
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 14(4P15.2) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4P15.2) MUTATED   142 105
  DEL PEAK 14(4P15.2) WILD-TYPE 212 116
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          247                           328 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          105                           116 
$`DEL PEAK 14(4P15.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        14.30        58.55         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21        32.45        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       20.78        20.12        18.64         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82         9.96         4.67        12.16        44.75        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.22         3.16         8.94        24.00         4.70 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       21.01        47.93         3.32         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.43         7.40         3.95        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.55        13.22         5.49         8.71        13.41        27.12 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.43         0.10        15.35         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        12.76         0.10        15.52        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-R6-A6DN 
       25.25        12.00        12.23        13.18         0.13         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59         5.06         7.04         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        1.45        12.69         7.00        20.38         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        18.18        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       11.24        15.91         3.42        11.01         9.44         6.61 
TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 
        7.43         9.57        17.29         9.17        31.20         9.21 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       28.01        18.15        28.73         9.07        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.69         9.60         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 
        7.40        22.19        17.52        14.04        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 
        5.39         9.21         0.49        11.54         9.86        15.68 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
       10.68         7.53        22.26         1.48         0.72         0.66 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       13.51         0.46        13.64         3.25         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.13         0.10         0.13         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        9.34        11.31        11.61        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        47.05        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 
       18.97         7.07        30.97        15.02        19.13        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8578 
       17.19        10.26        15.22        11.31        19.50        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C 
       16.44        11.31         7.40         0.62         7.99        11.38 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 
       14.07        17.06         5.52         0.23        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        12.59        14.17        12.10        22.75        25.81 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO 
        9.67        27.42        21.21        18.81         5.36         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A663 
        6.44         6.74         2.53         5.56        60.56         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
       45.67        18.21         6.08         9.24        11.05        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU 
       37.91       115.69         8.94        35.61         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        18.48        21.73         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PZ 
       22.19        12.79         2.70        17.85         1.87        65.16 
TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 
       36.69        36.16         9.50         9.73         9.04         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        42.54        11.24        22.09        32.94        29.98 
TCGA-VQ-AA6F 
       54.12 

$`DEL PEAK 14(4P15.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A4QT 
       31.27         7.63         7.69         6.21         2.63         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       17.03        23.41        14.86        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28        30.25         0.30         4.31         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        19.99        18.35         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50         2.66        13.48         7.76        21.37 
TCGA-L5-A8NU TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 
       83.24        13.41        13.15         0.10        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY 
       22.39        11.54        12.33         4.47        10.52        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 
       33.11         5.16         7.82        14.70        29.59        53.95 
TCGA-R6-A8W5 TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX 
       15.78        20.02         5.29        15.35        18.81        28.11 
TCGA-VR-A8EY TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       30.71         9.17        10.16         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        13.68        19.33        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       30.90        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 
       15.42        15.32        12.43         3.45        12.76        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        13.08         0.26         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 
       13.45         6.28         7.53        15.81        16.44         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4PD 
        8.98        14.17         0.53        12.82        19.36        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.42         1.15        11.57         5.13         2.83        13.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.07         0.07         0.10         0.16         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         3.42        12.43         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
        3.02        27.02        15.95         1.02        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       21.99         0.00         9.01        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        11.93        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85        13.35        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       10.55        12.33        24.72        16.80        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 
        5.03        13.58         0.56        18.08        14.27        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        10.19        19.36        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39        18.38         5.19        13.08        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A93G 
        6.51         5.56         1.81         7.82        13.51        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       37.64         3.72        19.73         8.52        61.25         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E2 
       57.44        16.87        19.04         0.92        48.79        35.24 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       27.35        64.57        14.33        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z 
       18.74        20.81        22.68         1.71         7.36        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        64.18         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        40.08        28.41        17.13        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                        12.00                         13.41 
[1] "0.1 - 115.7 (12.0)" "0.0 - 122.3 (13.4)"
[1] "hr=" "1.4"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4P15.2) MUTATED         4        3       17       15        40
  DEL PEAK 14(4P15.2) WILD-TYPE       7       16       31       17        37
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(4P15.2) MUTATED          33        16         42         29
  DEL PEAK 14(4P15.2) WILD-TYPE        51        13         55         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(4P15.2) MUTATED           20       19         1
  DEL PEAK 14(4P15.2) WILD-TYPE         28       32         3
D53V3, multiclass
            clus
vv           DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  STAGE I                              4                             7
  STAGE IA                             3                            16
  STAGE IB                            17                            31
  STAGE II                            15                            17
  STAGE IIA                           40                            37
  STAGE IIB                           33                            51
  STAGE III                           16                            13
  STAGE IIIA                          42                            55
  STAGE IIIB                          29                            43
  STAGE IIIC                          20                            28
  STAGE IV                            19                            32
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 14(4P15.2) MUTATED      17  51 130  45
  DEL PEAK 14(4P15.2) WILD-TYPE    36  75 150  79
D53V4, multiclass
       clus
vv      DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  T0+T1                          17                            36
  T2                             51                            75
  T3                            130                           150
  T4                             45                            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(4P15.2) MUTATED    79  80  43  38
  DEL PEAK 14(4P15.2) WILD-TYPE 121 102  53  59
D53V5, multiclass
    clus
vv   DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  N0                          79                           121
  N1                          80                           102
  N2                          43                            53
  N3                          38                            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"
D53V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED   221  13
  DEL PEAK 14(4P15.2) WILD-TYPE 292  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED    221   13
  DEL PEAK 14(4P15.2) WILD-TYPE  292   26
   clus
vv  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  0                         221                           292
  1                          13                            26
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED    66 194
  DEL PEAK 14(4P15.2) WILD-TYPE 116 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED     66  194
  DEL PEAK 14(4P15.2) WILD-TYPE  116  233
        clus
vv       DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  FEMALE                          66                           116
  MALE                           194                           233
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 14(4P15.2) MUTATED                                      22
  DEL PEAK 14(4P15.2) WILD-TYPE                                    49
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(4P15.2) MUTATED                                                       54
  DEL PEAK 14(4P15.2) WILD-TYPE                                                    108
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(4P15.2) MUTATED                                                                  34
  DEL PEAK 14(4P15.2) WILD-TYPE                                                                47
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 14(4P15.2) MUTATED                                                 31
  DEL PEAK 14(4P15.2) WILD-TYPE                                               47
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 14(4P15.2) MUTATED                                                          9
  DEL PEAK 14(4P15.2) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 14(4P15.2) MUTATED                                                           2
  DEL PEAK 14(4P15.2) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 14(4P15.2) MUTATED                                          8
  DEL PEAK 14(4P15.2) WILD-TYPE                                        5
D53V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 14(4P15.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    8
                                                                   clus
vv                                                                  DEL PEAK 14(4P15.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED     2 258
  DEL PEAK 14(4P15.2) WILD-TYPE   4 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED      2  258
  DEL PEAK 14(4P15.2) WILD-TYPE    4  345
     clus
vv    DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  NO                            2                             4
  YES                         258                           345
[1] 2 2
[1] FALSE
D53V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(4P15.2) MUTATED   124   7   6   9
  DEL PEAK 14(4P15.2) WILD-TYPE 223  11  13  16
D53V11, multiclass
    clus
vv   DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  R0                         124                           223
  R1                           7                            11
  R2                           6                            13
  RX                           9                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(4P15.2) MUTATED      63                         5
  DEL PEAK 14(4P15.2) WILD-TYPE    66                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(4P15.2) MUTATED                                           0   158
  DEL PEAK 14(4P15.2) WILD-TYPE                                         1   227
D53V13, multiclass
                                           clus
vv                                          DEL PEAK 14(4P15.2) MUTATED
  ASIAN                                                              63
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             158
                                           clus
vv                                          DEL PEAK 14(4P15.2) WILD-TYPE
  ASIAN                                                                66
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED     3 165
  DEL PEAK 14(4P15.2) WILD-TYPE   4 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED      3  165
  DEL PEAK 14(4P15.2) WILD-TYPE    4  229
                        clus
vv                       DEL PEAK 14(4P15.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         165
                        clus
vv                       DEL PEAK 14(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           229
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 15(4Q22.1) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(4Q22.1) MUTATED   162 114
  DEL PEAK 15(4Q22.1) WILD-TYPE 192 107
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          276                           299 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          114                           107 
$`DEL PEAK 15(4Q22.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 
        0.85         3.88         0.53         0.79        12.82         4.67 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E 
       12.16        44.75        60.39        42.77        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        3.16         4.31         8.94        24.00         4.70         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38         3.16        58.59         4.90         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         7.40         3.95        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR 
       35.97        12.92        13.48        16.47        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
        5.92        10.45        12.66        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.59        12.76         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.00        13.18 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30        15.78         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         4.80         9.27         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       22.82         1.55        28.11        42.87        15.06        11.24 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       15.91         3.42         2.66        11.01         9.44         6.61 
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6803 
       18.35        17.29        19.33         9.17        21.11        31.20 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.01        18.15         9.07        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.69         9.60        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
       15.58        19.50        22.19        17.52        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 
        3.72         5.39        25.18         9.21        20.22        15.81 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       11.54         9.86        10.68         7.53        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.72         0.66        13.51         1.15        13.64         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.13         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
       11.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
        3.02         7.99         8.05        54.08         4.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       19.07        12.03        18.97         7.07        22.98        30.97 
TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 
        0.99        12.03        79.07         4.01        69.04        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       12.66        11.93        19.13        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 
       15.22        15.98        10.55        11.31        19.50        18.21 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       16.44        11.31         7.40         0.62         7.99        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
       11.38         3.48        19.53        14.07        17.06        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        5.52         0.23         1.51         5.92        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU 
       12.10         0.76         5.59        22.75         8.98         6.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO 
       27.42        21.21        18.81         3.39         5.36         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A663 TCGA-R5-A7O7 
        6.44         6.74         5.56         2.53         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 
       18.21         6.08         9.24        11.05         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DV 
       37.91       115.69         8.94        35.61        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.02        18.48        35.24        21.73         7.73        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       12.79         2.70         9.27        13.35        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       36.69        18.74        20.81         9.50         9.73        52.24 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 
        4.54         5.72        21.04        42.54        22.09        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        29.98        54.12        16.14        21.11        12.43 

$`DEL PEAK 15(4Q22.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       58.55         7.69         6.21        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
       18.64         9.30        17.03        23.41         9.96        14.86 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.50       122.10        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       21.70        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        7.17        29.00         8.71        25.12         0.36         3.02 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-LN-A49N TCGA-LN-A49S 
       13.55         7.76         5.49        21.37        12.43        13.15 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10         0.10        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       11.54        13.22        12.23        12.03         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB 
        5.16         7.82        14.70        53.95         2.89         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        3.42        15.35        12.43        18.31         8.12        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       18.18        46.19         9.17        10.16         2.10        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       25.61        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 
       15.42        15.32        28.73        12.43         3.45        12.76 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8297 
       11.44        12.26        20.55         8.05         0.56         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        13.08         0.26         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        3.32        11.80        19.17         0.26        15.85         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44        15.68         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        12.82        19.36         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 
       11.57         2.83        13.18         0.07         0.13         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
        0.10         3.42         9.34         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
       15.95         1.02        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
        9.01        12.00         6.97        36.00         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        7.99        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       12.79        12.33        24.72        16.80        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
       21.27        22.29        59.54         5.03         0.56        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 
       26.47        14.27        11.41        10.62        24.30        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.98         0.10         6.51        10.19        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        8.81         3.45        18.38         5.19        13.08        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       20.15        37.64         3.72        19.73         8.52        61.25 
TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.60         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU 
       57.44        16.87        19.04         5.79         0.92         5.46 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       22.19         2.50        17.85         1.87        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       26.24        27.35        64.57        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 
       22.68         1.71        36.16         7.36         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
       55.43         6.58        64.18         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        17.13        26.04        10.62         0.79 

  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                        12.33                         13.35 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.3)"
[1] "hr=" "1.3"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(4Q22.1) MUTATED         2        5       18       18        37
  DEL PEAK 15(4Q22.1) WILD-TYPE       9       14       30       14        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(4Q22.1) MUTATED          41        20         49         31
  DEL PEAK 15(4Q22.1) WILD-TYPE        43         9         48         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(4Q22.1) MUTATED           21       24         4
  DEL PEAK 15(4Q22.1) WILD-TYPE         27       27         0
D54V3, multiclass
            clus
vv           DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             5                            14
  STAGE IB                            18                            30
  STAGE II                            18                            14
  STAGE IIA                           37                            40
  STAGE IIB                           41                            43
  STAGE III                           20                             9
  STAGE IIIA                          49                            48
  STAGE IIIB                          31                            41
  STAGE IIIC                          21                            27
  STAGE IV                            24                            27
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 15(4Q22.1) MUTATED      16  59 148  50
  DEL PEAK 15(4Q22.1) WILD-TYPE    37  67 132  74
D54V4, multiclass
       clus
vv      DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  T0+T1                          16                            37
  T2                             59                            67
  T3                            148                           132
  T4                             50                            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 15(4Q22.1) MUTATED    85  92  51  43
  DEL PEAK 15(4Q22.1) WILD-TYPE 115  90  45  54
D54V5, multiclass
    clus
vv   DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  N0                          85                           115
  N1                          92                            90
  N2                          51                            45
  N3                          43                            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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED   242  18
  DEL PEAK 15(4Q22.1) WILD-TYPE 271  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED    242   18
  DEL PEAK 15(4Q22.1) WILD-TYPE  271   21
   clus
vv  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  0                         242                           271
  1                          18                            21
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED    77 213
  DEL PEAK 15(4Q22.1) WILD-TYPE 105 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED     77  213
  DEL PEAK 15(4Q22.1) WILD-TYPE  105  214
        clus
vv       DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  FEMALE                          77                           105
  MALE                           213                           214
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 15(4Q22.1) MUTATED                                      23
  DEL PEAK 15(4Q22.1) WILD-TYPE                                    48
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(4Q22.1) MUTATED                                                       66
  DEL PEAK 15(4Q22.1) WILD-TYPE                                                     96
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(4Q22.1) MUTATED                                                                  41
  DEL PEAK 15(4Q22.1) WILD-TYPE                                                                40
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 15(4Q22.1) MUTATED                                                 37
  DEL PEAK 15(4Q22.1) WILD-TYPE                                               41
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 15(4Q22.1) MUTATED                                                          9
  DEL PEAK 15(4Q22.1) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 15(4Q22.1) MUTATED                                                           5
  DEL PEAK 15(4Q22.1) WILD-TYPE                                                         3
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 15(4Q22.1) MUTATED                                          8
  DEL PEAK 15(4Q22.1) WILD-TYPE                                        5
D54V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 15(4Q22.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    8
                                                                   clus
vv                                                                  DEL PEAK 15(4Q22.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED     4 286
  DEL PEAK 15(4Q22.1) WILD-TYPE   2 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED      4  286
  DEL PEAK 15(4Q22.1) WILD-TYPE    2  317
     clus
vv    DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  NO                            4                             2
  YES                         286                           317
[1] 2 2
[1] FALSE
D54V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(4Q22.1) MUTATED   146  10  10   8
  DEL PEAK 15(4Q22.1) WILD-TYPE 201   8   9  17
D54V11, multiclass
    clus
vv   DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  R0                         146                           201
  R1                          10                             8
  R2                          10                             9
  RX                           8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(4Q22.1) MUTATED      67                         7
  DEL PEAK 15(4Q22.1) WILD-TYPE    62                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(4Q22.1) MUTATED                                           1   175
  DEL PEAK 15(4Q22.1) WILD-TYPE                                         0   210
D54V13, multiclass
                                           clus
vv                                          DEL PEAK 15(4Q22.1) MUTATED
  ASIAN                                                              67
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             175
                                           clus
vv                                          DEL PEAK 15(4Q22.1) WILD-TYPE
  ASIAN                                                                62
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED     3 179
  DEL PEAK 15(4Q22.1) WILD-TYPE   4 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED      3  179
  DEL PEAK 15(4Q22.1) WILD-TYPE    4  215
                        clus
vv                       DEL PEAK 15(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         179
                        clus
vv                       DEL PEAK 15(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           215
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 16(4Q34.3) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(4Q34.3) MUTATED   164 116
  DEL PEAK 16(4Q34.3) WILD-TYPE 190 105
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          280                           295 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          116                           105 
$`DEL PEAK 16(4Q34.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 
       32.45        33.27         0.85         3.88         0.53         0.79 
TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
       12.82        44.75        60.39        41.52        42.77        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       25.22         3.16         4.31         8.94        24.00         4.70 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW 
       18.35         3.32         3.16        58.59         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE 
        7.43         6.94         0.36         7.40         3.95        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       10.36         5.92        10.45        12.66        13.41         0.10 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.59        12.76        22.39         0.10        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        10.52        12.00        12.23        13.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35         9.30         2.89         1.45        12.69 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00        20.02        20.38         4.80         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       19.96        22.82         1.55         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TJ 
       42.87        15.06        15.91        19.73        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 
        9.44        18.35        17.29        19.33         9.17        25.61 
TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       12.16        31.20         9.21        35.24        15.42        18.15 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73        12.43         9.07        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.69         9.60         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
        7.40        19.50        22.19        17.52        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 
        3.72         5.39        25.18         9.21        20.22         0.49 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       11.54         9.86         7.53        22.26         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        0.66        13.51        20.65         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.10         0.16         0.10         0.13         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 
       11.31        12.43        11.61        12.20        20.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       12.03         9.01        18.97        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6525 
        1.02        15.02        79.07        12.66        19.13        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-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV 
       12.33        19.50        18.21        14.27        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31        11.44         2.96         7.40         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
       16.24        11.38        19.53        14.07        17.06        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        5.52         0.23         1.51         5.92        12.59        12.10 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        0.76        22.75         8.98         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ 
       12.95        23.84        12.30         9.67        27.42         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
        5.19        13.08         1.41         6.44         6.74         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.81         2.53        60.56         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52         6.08         9.24        11.05        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       37.91         8.94        35.61         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.02        18.48        35.24        21.73         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       22.19        12.79        13.35        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       36.69        18.74        22.68         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
       52.24         4.54        21.04        42.54        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       40.08        32.94        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        21.11        12.43         0.79 

$`DEL PEAK 16(4Q34.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IC-A6RF 
       31.27        58.55         7.63        13.94         7.69         6.21 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       20.09        20.78         2.63        20.12        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       17.03        23.41         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A938 TCGA-JY-A939 
       12.16       122.10        68.02         3.68        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        24.03         6.28        30.25         0.30         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        19.99        21.01        47.93         7.17         1.38 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NK 
       29.00         8.71         2.60        25.12         3.02        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U 
        7.76        21.37        52.57        12.43        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10         0.10        12.46        12.49        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       11.54        13.22        25.25        12.03         0.13        33.11 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       14.70        53.95        15.78         5.29         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B 
       18.81        12.43        18.31        30.71        46.19        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 
        9.17        10.16         3.42         2.10         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70         9.47         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 
       13.87        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        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        15.32         3.45        12.76 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        13.08         0.26         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        3.32        11.80        19.17         0.26        15.85         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53        12.82        19.36         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8529 TCGA-CD-8531 
       11.57         5.13         2.83        13.18         0.13         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         3.42         9.34         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 
        3.02        15.95         1.02        14.01        29.98        21.99 
TCGA-CG-4462 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        0.00         7.07        12.00        36.00         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 
       69.04        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        14.66        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-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         7.13        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
        3.48        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-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
        3.39        18.38        12.59         6.51         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI 
        5.56        20.15        37.64         3.72        19.73        61.25 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.60         8.61         5.13        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DU 
       71.38        57.44        16.87        19.04         5.79         5.46 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        26.24        14.33        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       20.81        36.16         7.36         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 
        6.58         5.72        64.18         2.66        11.24        28.41 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                        122.3                         122.1 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                        12.43                         13.15 
[1] "0.1 - 122.3 (12.4)" "0.0 - 122.1 (13.2)"
[1] "hr=" "1.3"
D55V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(4Q34.3) MUTATED         2        5       20       21        34
  DEL PEAK 16(4Q34.3) WILD-TYPE       9       14       28       11        43
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(4Q34.3) MUTATED          35        20         48         37
  DEL PEAK 16(4Q34.3) WILD-TYPE        49         9         49         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(4Q34.3) MUTATED           28       17         3
  DEL PEAK 16(4Q34.3) WILD-TYPE         20       34         1
D55V3, multiclass
            clus
vv           DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             5                            14
  STAGE IB                            20                            28
  STAGE II                            21                            11
  STAGE IIA                           34                            43
  STAGE IIB                           35                            49
  STAGE III                           20                             9
  STAGE IIIA                          48                            49
  STAGE IIIB                          37                            35
  STAGE IIIC                          28                            20
  STAGE IV                            17                            34
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 16(4Q34.3) MUTATED      19  56 141  58
  DEL PEAK 16(4Q34.3) WILD-TYPE    34  70 139  66
D55V4, multiclass
       clus
vv      DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  T0+T1                          19                            34
  T2                             56                            70
  T3                            141                           139
  T4                             58                            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 16(4Q34.3) MUTATED    85  90  48  49
  DEL PEAK 16(4Q34.3) WILD-TYPE 115  92  48  48
D55V5, multiclass
    clus
vv   DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  N0                          85                           115
  N1                          90                            92
  N2                          48                            48
  N3                          49                            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"
D55V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED   244  15
  DEL PEAK 16(4Q34.3) WILD-TYPE 269  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED    244   15
  DEL PEAK 16(4Q34.3) WILD-TYPE  269   24
   clus
vv  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  0                         244                           269
  1                          15                            24
[1] 2 2
[1] FALSE
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED    85 207
  DEL PEAK 16(4Q34.3) WILD-TYPE  97 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED     85  207
  DEL PEAK 16(4Q34.3) WILD-TYPE   97  220
        clus
vv       DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  FEMALE                          85                            97
  MALE                           207                           220
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 16(4Q34.3) MUTATED                                      21
  DEL PEAK 16(4Q34.3) WILD-TYPE                                    50
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(4Q34.3) MUTATED                                                       66
  DEL PEAK 16(4Q34.3) WILD-TYPE                                                     96
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(4Q34.3) MUTATED                                                                  48
  DEL PEAK 16(4Q34.3) WILD-TYPE                                                                33
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 16(4Q34.3) MUTATED                                                 42
  DEL PEAK 16(4Q34.3) WILD-TYPE                                               36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 16(4Q34.3) MUTATED                                                          8
  DEL PEAK 16(4Q34.3) WILD-TYPE                                                       13
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 16(4Q34.3) MUTATED                                                           4
  DEL PEAK 16(4Q34.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 16(4Q34.3) MUTATED                                          7
  DEL PEAK 16(4Q34.3) WILD-TYPE                                        6
D55V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 16(4Q34.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     66
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    7
                                                                   clus
vv                                                                  DEL PEAK 16(4Q34.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED     4 288
  DEL PEAK 16(4Q34.3) WILD-TYPE   2 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED      4  288
  DEL PEAK 16(4Q34.3) WILD-TYPE    2  315
     clus
vv    DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  NO                            4                             2
  YES                         288                           315
[1] 2 2
[1] FALSE
D55V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(4Q34.3) MUTATED   160   8   6   6
  DEL PEAK 16(4Q34.3) WILD-TYPE 187  10  13  19
D55V11, multiclass
    clus
vv   DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  R0                         160                           187
  R1                           8                            10
  R2                           6                            13
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(4Q34.3) MUTATED      65                         7
  DEL PEAK 16(4Q34.3) WILD-TYPE    64                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(4Q34.3) MUTATED                                           0   183
  DEL PEAK 16(4Q34.3) WILD-TYPE                                         1   202
D55V13, multiclass
                                           clus
vv                                          DEL PEAK 16(4Q34.3) MUTATED
  ASIAN                                                              65
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             183
                                           clus
vv                                          DEL PEAK 16(4Q34.3) WILD-TYPE
  ASIAN                                                                64
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED     3 179
  DEL PEAK 16(4Q34.3) WILD-TYPE   4 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED      3  179
  DEL PEAK 16(4Q34.3) WILD-TYPE    4  215
                        clus
vv                       DEL PEAK 16(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         179
                        clus
vv                       DEL PEAK 16(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           215
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 17(5Q12.1) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(5Q12.1) MUTATED   157 104
  DEL PEAK 17(5Q12.1) WILD-TYPE 197 117
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          261                           314 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          104                           117 
$`DEL PEAK 17(5Q12.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A8O2 
        0.85         2.63         3.88         0.53        17.03         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
      122.10        44.75        60.39        42.77        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS 
       21.01        47.93         3.32         7.17         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.13         2.60         0.36         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
        5.49        21.37         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        12.43         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
       13.15        15.35         0.10        13.25        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39        15.52        12.33         4.47        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 
       10.52        12.00        12.23        12.03        13.18        33.11 
TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.16         5.06        29.59         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RC TCGA-V5-AASW 
        2.89         1.45        12.69        20.02         3.42         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        4.44        18.81        19.96        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
        8.12        28.11        42.87        11.24        15.91         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        19.56        11.01         9.44         6.61 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       19.33         9.17        12.16        35.24        15.42        28.01 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 
        3.45        12.76        18.71        11.44         0.69        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
        2.66         2.20        14.04        14.79         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       20.22        11.54         9.86         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PE TCGA-BR-A4PF 
        7.53        22.26         1.48         0.72        20.42         1.15 
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-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.07         0.10         0.13         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 
        9.34        11.31        11.61        12.20        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        36.00        15.02        69.04        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         7.99        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         5.52         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 
       23.84         9.67        27.42        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR 
       18.38         5.19        13.08         6.44         6.74         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        5.56         7.82         2.53        60.56        37.64         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       45.67        18.21         8.52        37.91       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.79         5.46        13.25        13.02        35.24        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N 
        1.87        13.35        27.35        14.33        36.69        18.74 
TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 
        1.71         9.73        52.24         9.04         4.54         5.72 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       21.04        42.54        18.41        40.08        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       54.12        21.11         0.79 

$`DEL PEAK 17(5Q12.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       31.27         7.69         6.21        20.78        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       14.50        12.16        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        23.18        24.03         6.28         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX 
        8.94        19.99        18.35         1.38        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NL 
        6.94         8.71        25.12         7.40        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49X TCGA-LN-A4A1 
        7.76        83.24        12.66        13.41         0.10        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A9FO 
       12.76        12.59         0.10        11.54        13.22         0.13 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 
        7.82         8.02         7.59        14.70         7.04        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET 
        7.00        20.38         5.29         4.80        15.35         1.55 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       30.71        18.18        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
        3.42        26.70        11.70         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       26.10        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93        18.15        15.32        28.73        12.43 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        9.07        17.49        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        16.31        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72        25.18         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       16.44        15.68        12.56         6.08        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51         0.46        20.65        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        2.83         3.25         0.07         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.10        12.43         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02         3.02        15.95         1.02         8.05        54.08 
TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        21.99         0.00         9.01         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       12.03        28.96        79.07        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99        12.36        12.66        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61        17.85        10.55        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
        9.76         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 
        5.03         0.23        18.08        26.47        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.10        10.62        24.30        12.30        11.84        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        0.26        19.36        12.30         8.88         8.81         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 
        5.36         1.41        12.59         1.81        13.51         5.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       20.15         3.72        19.73        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       19.04         0.92        48.79        18.48        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO 
       32.48        28.96        34.29        16.31         2.50         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       23.41        15.65        26.24        64.57        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        20.81        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.50         2.01        55.43         6.58        64.18         2.66 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       11.24        22.09        28.41        29.98        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                        122.1                         122.3 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                       12.460                        12.855 
[1] "0.1 - 122.1 (12.5)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D56V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(5Q12.1) MUTATED         9        8       14       11        32
  DEL PEAK 17(5Q12.1) WILD-TYPE       2       11       34       21        45
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(5Q12.1) MUTATED          41        18         49         29
  DEL PEAK 17(5Q12.1) WILD-TYPE        43        11         48         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(5Q12.1) MUTATED           18       22         3
  DEL PEAK 17(5Q12.1) WILD-TYPE         30       29         1
D56V3, multiclass
            clus
vv           DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  STAGE I                              9                             2
  STAGE IA                             8                            11
  STAGE IB                            14                            34
  STAGE II                            11                            21
  STAGE IIA                           32                            45
  STAGE IIB                           41                            43
  STAGE III                           18                            11
  STAGE IIIA                          49                            48
  STAGE IIIB                          29                            43
  STAGE IIIC                          18                            30
  STAGE IV                            22                            29
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 17(5Q12.1) MUTATED      28  54 132  43
  DEL PEAK 17(5Q12.1) WILD-TYPE    25  72 148  81
D56V4, multiclass
       clus
vv      DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  T0+T1                          28                            25
  T2                             54                            72
  T3                            132                           148
  T4                             43                            81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(5Q12.1) MUTATED    82  89  45  39
  DEL PEAK 17(5Q12.1) WILD-TYPE 118  93  51  58
D56V5, multiclass
    clus
vv   DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  N0                          82                           118
  N1                          89                            93
  N2                          45                            51
  N3                          39                            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"
D56V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED   225  18
  DEL PEAK 17(5Q12.1) WILD-TYPE 288  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED    225   18
  DEL PEAK 17(5Q12.1) WILD-TYPE  288   21
   clus
vv  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  0                         225                           288
  1                          18                            21
[1] 2 2
[1] FALSE
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED    71 200
  DEL PEAK 17(5Q12.1) WILD-TYPE 111 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED     71  200
  DEL PEAK 17(5Q12.1) WILD-TYPE  111  227
        clus
vv       DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  FEMALE                          71                           111
  MALE                           200                           227
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 17(5Q12.1) MUTATED                                      11
  DEL PEAK 17(5Q12.1) WILD-TYPE                                    60
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(5Q12.1) MUTATED                                                       59
  DEL PEAK 17(5Q12.1) WILD-TYPE                                                    103
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(5Q12.1) MUTATED                                                                  33
  DEL PEAK 17(5Q12.1) WILD-TYPE                                                                48
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 17(5Q12.1) MUTATED                                                 44
  DEL PEAK 17(5Q12.1) WILD-TYPE                                               34
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 17(5Q12.1) MUTATED                                                         10
  DEL PEAK 17(5Q12.1) WILD-TYPE                                                       11
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 17(5Q12.1) MUTATED                                                           4
  DEL PEAK 17(5Q12.1) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 17(5Q12.1) MUTATED                                          4
  DEL PEAK 17(5Q12.1) WILD-TYPE                                        9
D56V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 17(5Q12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 17(5Q12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED     3 268
  DEL PEAK 17(5Q12.1) WILD-TYPE   3 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED      3  268
  DEL PEAK 17(5Q12.1) WILD-TYPE    3  335
     clus
vv    DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  NO                            3                             3
  YES                         268                           335
[1] 2 2
[1] FALSE
D56V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(5Q12.1) MUTATED   134   9   6   5
  DEL PEAK 17(5Q12.1) WILD-TYPE 213   9  13  20
D56V11, multiclass
    clus
vv   DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  R0                         134                           213
  R1                           9                             9
  R2                           6                            13
  RX                           5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(5Q12.1) MUTATED      64                         6
  DEL PEAK 17(5Q12.1) WILD-TYPE    65                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(5Q12.1) MUTATED                                           0   166
  DEL PEAK 17(5Q12.1) WILD-TYPE                                         1   219
D56V13, multiclass
                                           clus
vv                                          DEL PEAK 17(5Q12.1) MUTATED
  ASIAN                                                              64
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             166
                                           clus
vv                                          DEL PEAK 17(5Q12.1) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED     3 161
  DEL PEAK 17(5Q12.1) WILD-TYPE   4 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED      3  161
  DEL PEAK 17(5Q12.1) WILD-TYPE    4  233
                        clus
vv                       DEL PEAK 17(5Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         161
                        clus
vv                       DEL PEAK 17(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           233
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 18(6P25.3) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(6P25.3) MUTATED    99  75
  DEL PEAK 18(6P25.3) WILD-TYPE 255 146
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          174                           401 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           75                           146 
$`DEL PEAK 18(6P25.3) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         7.63        13.94         8.94         4.21 
TCGA-IG-A3I8 TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97I 
       33.27        18.64         3.88         0.53        23.41        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E 
      122.10        60.39        23.18        31.56         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30         4.31         4.70        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A88Y TCGA-L5-A8NF TCGA-L5-A8NG 
        1.38         3.16         7.13         0.36         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT 
       13.48        16.47        13.55        13.22        13.41        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A49W 
       52.57        10.36         5.92        12.43         0.10        13.25 
TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.49        12.33        25.25        13.18        33.11         5.16 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        7.59        14.70         9.30        15.78         2.89        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       12.43        18.31         8.12        18.18        15.06        11.24 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6458 
        2.66        19.73        26.70         6.97        17.29        19.33 
TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8360 
       12.16        31.20        28.01         3.45         0.69         6.18 
TCGA-BR-8361 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
       19.50         9.21        20.22        11.54         9.86         8.22 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       22.26         1.48        12.89         0.72        13.51        20.65 
TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 
        1.15        13.15         0.30         0.07         0.07         0.10 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4466 
        0.13         9.34        11.31        12.43         8.05        18.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5578 
        1.02        12.03        79.07        65.10        69.04        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 
       19.13        20.55        18.84        18.54        13.35        15.22 
TCGA-D7-6815 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO 
       15.98        11.31        11.44        15.65         7.40        16.24 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 
       72.23        11.38        17.06        13.58        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
        5.92        12.10         5.59        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL 
        6.25        12.95         9.67        27.42         5.36         5.19 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        1.41         6.74         1.81         5.56        45.67        18.21 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 
        6.08         9.24        16.67       122.30       115.69        57.44 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        8.94         0.92         5.46        32.48         7.73        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY 
        2.70        17.85         1.87        13.35        27.35        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94R 
       18.74        20.81        52.24         9.04         5.72        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       40.08        32.94        54.12        26.04        16.14         0.79 

$`DEL PEAK 18(6P25.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       25.78        31.27         5.92        16.24        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        6.21        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        44.75        68.02         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       42.77        25.41        21.70        25.22        24.03         6.28 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         3.68        32.61        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
       47.93        58.59         4.90        29.00         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       55.50        12.92         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       83.24        46.09        10.45        12.66        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.15        15.35         0.10        12.46        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        10.52        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.13         7.82         8.02         5.06         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASX 
        6.35        53.95         1.45         7.00         4.80         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       18.81        19.96        22.82         1.55        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       42.87        46.19         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        2.10        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.61         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43        11.44        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         7.40        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        6.28         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-A4IU 
       10.68        12.56        13.87         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         8.98        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-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-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
        2.83         3.25        13.18         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-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        3.42        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         0.00         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 
        0.99       105.07        15.02        28.96         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
        7.99        12.36        11.93        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       14.76        13.71        11.24         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
        4.34         7.13         0.62         7.99        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.56         5.52         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 
       23.84        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        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.51         5.56         7.82        13.51         2.53        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       20.15        37.64         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW 
       61.25         4.60        11.05         8.61         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64       116.38        71.38        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79        48.79        13.25        13.02        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        34.45        27.88        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50        12.79         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       26.24        64.57        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.73         2.01        55.43         4.54         6.58        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
       21.04         2.66        11.24        22.09        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       29.98        17.13        21.11        12.43        10.62 

  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                       122.30                        116.38 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                        12.79                         12.76 
[1] "0.1 - 122.3 (12.8)" "0.0 - 116.4 (12.8)"
[1] "hr=" "1.1"
D57V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6P25.3) MUTATED         5        6        9        6        23
  DEL PEAK 18(6P25.3) WILD-TYPE       6       13       39       26        54
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6P25.3) MUTATED          26        12         29         20
  DEL PEAK 18(6P25.3) WILD-TYPE        58        17         68         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(6P25.3) MUTATED           15       14         2
  DEL PEAK 18(6P25.3) WILD-TYPE         33       37         2
D57V3, multiclass
            clus
vv           DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  STAGE I                              5                             6
  STAGE IA                             6                            13
  STAGE IB                             9                            39
  STAGE II                             6                            26
  STAGE IIA                           23                            54
  STAGE IIB                           26                            58
  STAGE III                           12                            17
  STAGE IIIA                          29                            68
  STAGE IIIB                          20                            52
  STAGE IIIC                          15                            33
  STAGE IV                            14                            37
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 18(6P25.3) MUTATED      17  35  93  27
  DEL PEAK 18(6P25.3) WILD-TYPE    36  91 187  97
D57V4, multiclass
       clus
vv      DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  T0+T1                          17                            36
  T2                             35                            91
  T3                             93                           187
  T4                             27                            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 18(6P25.3) MUTATED    57  52  30  29
  DEL PEAK 18(6P25.3) WILD-TYPE 143 130  66  68
D57V5, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  N0                          57                           143
  N1                          52                           130
  N2                          30                            66
  N3                          29                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED   146   8
  DEL PEAK 18(6P25.3) WILD-TYPE 367  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED    146    8
  DEL PEAK 18(6P25.3) WILD-TYPE  367   31
   clus
vv  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  0                         146                           367
  1                           8                            31
[1] 2 2
[1] FALSE
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED    53 129
  DEL PEAK 18(6P25.3) WILD-TYPE 129 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     53  129
  DEL PEAK 18(6P25.3) WILD-TYPE  129  298
        clus
vv       DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  FEMALE                          53                           129
  MALE                           129                           298
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 18(6P25.3) MUTATED                                      13
  DEL PEAK 18(6P25.3) WILD-TYPE                                    58
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6P25.3) MUTATED                                                       36
  DEL PEAK 18(6P25.3) WILD-TYPE                                                    126
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6P25.3) MUTATED                                                                  22
  DEL PEAK 18(6P25.3) WILD-TYPE                                                                59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 18(6P25.3) MUTATED                                                 33
  DEL PEAK 18(6P25.3) WILD-TYPE                                               45
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 18(6P25.3) MUTATED                                                          4
  DEL PEAK 18(6P25.3) WILD-TYPE                                                       17
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 18(6P25.3) MUTATED                                                           2
  DEL PEAK 18(6P25.3) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 18(6P25.3) MUTATED                                          2
  DEL PEAK 18(6P25.3) WILD-TYPE                                       11
D57V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 18(6P25.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 18(6P25.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED     1 181
  DEL PEAK 18(6P25.3) WILD-TYPE   5 422
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED      1  181
  DEL PEAK 18(6P25.3) WILD-TYPE    5  422
     clus
vv    DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  NO                            1                             5
  YES                         181                           422
[1] 2 2
[1] FALSE
D57V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(6P25.3) MUTATED    90   7   2   6
  DEL PEAK 18(6P25.3) WILD-TYPE 257  11  17  19
D57V11, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  R0                          90                           257
  R1                           7                            11
  R2                           2                            17
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(6P25.3) MUTATED      37                         4
  DEL PEAK 18(6P25.3) WILD-TYPE    92                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(6P25.3) MUTATED                                           0   117
  DEL PEAK 18(6P25.3) WILD-TYPE                                         1   268
D57V13, multiclass
                                           clus
vv                                          DEL PEAK 18(6P25.3) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             117
                                           clus
vv                                          DEL PEAK 18(6P25.3) WILD-TYPE
  ASIAN                                                                92
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED     4 107
  DEL PEAK 18(6P25.3) WILD-TYPE   3 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED      4  107
  DEL PEAK 18(6P25.3) WILD-TYPE    3  287
                        clus
vv                       DEL PEAK 18(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         107
                        clus
vv                       DEL PEAK 18(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 19(6Q16.3) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(6Q16.3) MUTATED    80  55
  DEL PEAK 19(6Q16.3) WILD-TYPE 274 166
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          135                           440 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                           55                           166 
$`DEL PEAK 19(6Q16.3) MUTATED`
TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 
       25.78         7.69        33.27        20.09         0.53         4.67 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C 
       14.50        44.75        60.39        42.77        25.22         3.16 
TCGA-L5-A43M TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A8NJ TCGA-L5-A8NK 
        8.94        18.35         3.16         0.36        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R 
       13.22        13.41        83.24        52.57         5.92         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
       13.25         0.10        12.59        22.39        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.33        25.25         0.13         8.02         5.06        29.59 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW 
        2.89        12.69        20.02        20.38         3.42         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD 
       22.82        12.43        18.31         8.12        28.11         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 
        2.10        19.73        18.35         6.18        17.29         9.17 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8080 
       28.01        15.32         3.45        12.76        14.43         9.60 
TCGA-BR-8486 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       20.22         0.53        13.51        20.65        20.42         1.15 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4475 
        3.42         8.05        14.01        29.98        12.03        22.98 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 
       36.00         1.02        15.02        69.04        12.66        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8576 
       18.54        13.35        17.19        15.98        24.72        14.66 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7829 
       13.78        11.31        15.65         7.40        11.38        19.53 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4H4 
       17.06        13.58         0.56        26.47        22.75        23.84 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       12.30        21.21         5.19         1.41         6.44        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N5 
        5.56         1.81        18.21         6.08       122.30        57.44 
TCGA-SW-A7EA TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PS 
       19.04        18.48         7.73        46.26        12.79        13.35 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A923 
       27.35        14.33        18.74        20.81         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6I 
        4.54        21.04        18.41        40.08        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        10.62         0.79 

$`DEL PEAK 19(6Q16.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3Y9 
        8.94        16.24         4.21        32.45         6.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 
       12.16       122.10        68.02         3.68        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31        24.00         3.68         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        47.93         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        8.71         2.60        25.12         7.40         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM 
       55.50         2.66        35.97        12.92        13.48         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49        21.37         8.71        27.12        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        12.43        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
        0.10        12.46        12.49        12.76        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       15.52        11.54         4.47        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ 
       12.03        13.18        33.11         5.16         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
        1.45         7.00         5.29         4.80        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.81        19.96         1.55        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.44         6.61         6.97         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 
       15.42        18.15        28.73        12.43         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        11.44         0.69        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
       12.82         0.66        19.36         0.46        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 
        0.07         0.07         0.07         0.07         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       15.95         1.02         7.99        54.08         4.01        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        21.99         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00        30.97         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-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-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-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        10.26        15.22        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        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        8.38         4.34         7.13         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        21.27         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03         5.52         0.23        18.08         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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        19.36         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       13.08         6.74         6.51         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
        9.86        45.67         8.52        61.25         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        16.31        22.19         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       65.16        36.69        11.70        11.93        61.22        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        64.18         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       11.24        22.09        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                        122.3                         122.1 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                       13.510                        12.445 
[1] "0.1 - 122.3 (13.5)" "0.0 - 122.1 (12.4)"
[1] "hr=" "1.1"
D58V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q16.3) MUTATED         1        5       10        7        16
  DEL PEAK 19(6Q16.3) WILD-TYPE      10       14       38       25        61
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q16.3) MUTATED          23        10         25         15
  DEL PEAK 19(6Q16.3) WILD-TYPE        61        19         72         57
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(6Q16.3) MUTATED            8        7         1
  DEL PEAK 19(6Q16.3) WILD-TYPE         40       44         3
D58V3, multiclass
            clus
vv           DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  STAGE I                              1                            10
  STAGE IA                             5                            14
  STAGE IB                            10                            38
  STAGE II                             7                            25
  STAGE IIA                           16                            61
  STAGE IIB                           23                            61
  STAGE III                           10                            19
  STAGE IIIA                          25                            72
  STAGE IIIB                          15                            57
  STAGE IIIC                           8                            40
  STAGE IV                             7                            44
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 19(6Q16.3) MUTATED      12  32  70  18
  DEL PEAK 19(6Q16.3) WILD-TYPE    41  94 210 106
D58V4, multiclass
       clus
vv      DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  T0+T1                          12                            41
  T2                             32                            94
  T3                             70                           210
  T4                             18                           106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 19(6Q16.3) MUTATED    44  46  23  17
  DEL PEAK 19(6Q16.3) WILD-TYPE 156 136  73  80
D58V5, multiclass
    clus
vv   DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  N0                          44                           156
  N1                          46                           136
  N2                          23                            73
  N3                          17                            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"
D58V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED   116   4
  DEL PEAK 19(6Q16.3) WILD-TYPE 397  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED    116    4
  DEL PEAK 19(6Q16.3) WILD-TYPE  397   35
   clus
vv  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  0                         116                           397
  1                           4                            35
[1] 2 2
[1] FALSE
D58V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED    31 111
  DEL PEAK 19(6Q16.3) WILD-TYPE 151 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED     31  111
  DEL PEAK 19(6Q16.3) WILD-TYPE  151  316
        clus
vv       DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  FEMALE                          31                           151
  MALE                           111                           316
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 19(6Q16.3) MUTATED                                       6
  DEL PEAK 19(6Q16.3) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q16.3) MUTATED                                                       34
  DEL PEAK 19(6Q16.3) WILD-TYPE                                                    128
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q16.3) MUTATED                                                                  19
  DEL PEAK 19(6Q16.3) WILD-TYPE                                                                62
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 19(6Q16.3) MUTATED                                                 23
  DEL PEAK 19(6Q16.3) WILD-TYPE                                               55
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 19(6Q16.3) MUTATED                                                          5
  DEL PEAK 19(6Q16.3) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 19(6Q16.3) MUTATED                                                           1
  DEL PEAK 19(6Q16.3) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 19(6Q16.3) MUTATED                                          2
  DEL PEAK 19(6Q16.3) WILD-TYPE                                       11
D58V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 19(6Q16.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 19(6Q16.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED     1 141
  DEL PEAK 19(6Q16.3) WILD-TYPE   5 462
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED      1  141
  DEL PEAK 19(6Q16.3) WILD-TYPE    5  462
     clus
vv    DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  NO                            1                             5
  YES                         141                           462
[1] 2 2
[1] FALSE
D58V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(6Q16.3) MUTATED    79   2   1   5
  DEL PEAK 19(6Q16.3) WILD-TYPE 268  16  18  20
D58V11, multiclass
    clus
vv   DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  R0                          79                           268
  R1                           2                            16
  R2                           1                            18
  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"
D58V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(6Q16.3) MUTATED      31                         5
  DEL PEAK 19(6Q16.3) WILD-TYPE    98                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(6Q16.3) MUTATED                                           0    88
  DEL PEAK 19(6Q16.3) WILD-TYPE                                         1   297
D58V13, multiclass
                                           clus
vv                                          DEL PEAK 19(6Q16.3) MUTATED
  ASIAN                                                              31
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              88
                                           clus
vv                                          DEL PEAK 19(6Q16.3) WILD-TYPE
  ASIAN                                                                98
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               297
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED     1  90
  DEL PEAK 19(6Q16.3) WILD-TYPE   6 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED      1   90
  DEL PEAK 19(6Q16.3) WILD-TYPE    6  304
                        clus
vv                       DEL PEAK 19(6Q16.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          90
                        clus
vv                       DEL PEAK 19(6Q16.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 20(6Q26) MUTATION ANALYSIS
D59V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(6Q26) MUTATED    86  57
  DEL PEAK 20(6Q26) WILD-TYPE 268 164
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        143                         432 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                         57                         164 
$`DEL PEAK 20(6Q26) MUTATED`
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH 
       25.78        33.27        20.09         4.67        14.50        42.77 
TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OR 
       25.41        25.22         3.16         4.31         8.94         3.16 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        0.36         7.40        13.48        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W 
       13.41        83.24        52.57         5.92         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ 
        0.10        12.59        12.49        12.76        22.39        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-R6-A6DN TCGA-R6-A6XG 
       13.22        25.25        12.00        12.23         8.02        29.59 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
        1.45        12.69        20.38         3.42         4.80         9.27 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-Z6-A8JD TCGA-ZR-A9CJ 
       22.82        12.43         8.12        28.11         3.42        19.73 
TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7716 
       19.56         6.61        19.33         9.17        12.16        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 
       18.15        15.32        28.73        12.76         0.69         9.60 
TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 
       15.81        12.89        13.51        20.42         1.15        13.15 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.13         0.16         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4440 
        3.42         9.34         3.02        15.95         8.05         4.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
       29.98        12.03         7.07        12.00         6.97         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       12.03        15.02        69.04        12.66        20.55        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       13.35        17.19        24.72        19.50        18.21        14.66 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 
       11.31        11.44        15.65         7.40        11.38        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-A4G3 
       13.58         0.56         5.52         0.23        26.47         5.59 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT 
        6.25        23.84        27.42         5.19         6.44         5.56 
TCGA-IN-A7NU TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 
        1.81         9.86        45.67        18.21         6.08        16.67 
TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E2 
      122.30        57.44         8.94         0.92        13.02        35.24 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q 
        7.73        46.26         2.50        13.35        14.33        20.81 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
       52.24         2.01         4.54        21.04        42.54        40.08 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        54.12        16.14        21.11         0.79 

$`DEL PEAK 20(6Q26) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
        9.96        14.86        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02         3.68        41.52        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         6.28        30.25         0.30        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.70        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        3.32         7.17         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NW 
        7.76         5.49        21.37         8.71        27.12        46.09 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36        10.45        12.66        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       15.35         0.10        12.46        12.59         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ 
       11.54         4.47        12.33        10.52        12.03        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        0.13        33.11         5.16         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX 
        2.89         7.00        20.02         5.29        15.35         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
       18.81        19.96         1.55        18.31        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       10.16         2.10         2.66        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-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 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        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         3.45         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        11.44        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        12.95         2.66        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46        20.65        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.18         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 
        0.07         0.07         0.07         0.07         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
        0.10        12.62        20.02        27.02         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 
       54.08        14.01        47.05        19.07        21.99         0.00 
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        36.00         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-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        8.38         4.34         7.13         0.62         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
       22.29        59.54         5.03        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
        1.41         6.74        12.59         6.51         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73         8.52        61.25         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT 
       71.38        35.61        16.87        19.04         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        18.48        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH 
       32.48        28.96        34.29        16.31        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        27.35        64.57        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.50         9.73         9.04        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        11.24        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        32.94        29.98        26.04        12.43        10.62 

  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                       0.07                        0.00 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                      122.3                       122.1 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                     12.760                      12.725 
[1] "0.1 - 122.3 (12.8)" "0.0 - 122.1 (12.7)"
[1] "hr=" "1.1"
D59V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(6Q26) MUTATED         0        2        7        9        22
  DEL PEAK 20(6Q26) WILD-TYPE      11       17       41       23        55
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(6Q26) MUTATED          17        11         26         18
  DEL PEAK 20(6Q26) WILD-TYPE        67        18         71         54
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(6Q26) MUTATED           10       15         1
  DEL PEAK 20(6Q26) WILD-TYPE         38       36         3
D59V3, multiclass
            clus
vv           DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  STAGE I                            0                          11
  STAGE IA                           2                          17
  STAGE IB                           7                          41
  STAGE II                           9                          23
  STAGE IIA                         22                          55
  STAGE IIB                         17                          67
  STAGE III                         11                          18
  STAGE IIIA                        26                          71
  STAGE IIIB                        18                          54
  STAGE IIIC                        10                          38
  STAGE IV                          15                          36
  STAGE IVA                          1                           3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  DEL PEAK 20(6Q26) MUTATED       7  27  84  23
  DEL PEAK 20(6Q26) WILD-TYPE    46  99 196 101
D59V4, multiclass
       clus
vv      DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  T0+T1                         7                          46
  T2                           27                          99
  T3                           84                         196
  T4                           23                         101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 20(6Q26) MUTATED    45  44  25  25
  DEL PEAK 20(6Q26) WILD-TYPE 155 138  71  72
D59V5, multiclass
    clus
vv   DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  N0                        45                         155
  N1                        44                         138
  N2                        25                          71
  N3                        25                          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"
D59V6, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED   121   9
  DEL PEAK 20(6Q26) WILD-TYPE 392  30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED    121    9
  DEL PEAK 20(6Q26) WILD-TYPE  392   30
   clus
vv  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  0                       121                         392
  1                         9                          30
[1] 2 2
[1] FALSE
D59V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED    36 113
  DEL PEAK 20(6Q26) WILD-TYPE 146 314
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED     36  113
  DEL PEAK 20(6Q26) WILD-TYPE  146  314
        clus
vv       DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  FEMALE                        36                         146
  MALE                         113                         314
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 20(6Q26) MUTATED                                      10
  DEL PEAK 20(6Q26) WILD-TYPE                                    61
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(6Q26) MUTATED                                                       33
  DEL PEAK 20(6Q26) WILD-TYPE                                                    129
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(6Q26) MUTATED                                                                  18
  DEL PEAK 20(6Q26) WILD-TYPE                                                                63
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 20(6Q26) MUTATED                                                 28
  DEL PEAK 20(6Q26) WILD-TYPE                                               50
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 20(6Q26) MUTATED                                                          5
  DEL PEAK 20(6Q26) WILD-TYPE                                                       16
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 20(6Q26) MUTATED                                                           1
  DEL PEAK 20(6Q26) WILD-TYPE                                                         7
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 20(6Q26) MUTATED                                          5
  DEL PEAK 20(6Q26) WILD-TYPE                                        8
D59V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 20(6Q26) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  5
                                                                   clus
vv                                                                  DEL PEAK 20(6Q26) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED     2 147
  DEL PEAK 20(6Q26) WILD-TYPE   4 456
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED      2  147
  DEL PEAK 20(6Q26) WILD-TYPE    4  456
     clus
vv    DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  NO                          2                           4
  YES                       147                         456
[1] 2 2
[1] FALSE
D59V10, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(6Q26) MUTATED    81   6   5   3
  DEL PEAK 20(6Q26) WILD-TYPE 266  12  14  22
D59V11, multiclass
    clus
vv   DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  R0                        81                         266
  R1                         6                          12
  R2                         5                          14
  RX                         3                          22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(6Q26) MUTATED      34                         5
  DEL PEAK 20(6Q26) WILD-TYPE    95                         8
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(6Q26) MUTATED                                           0    87
  DEL PEAK 20(6Q26) WILD-TYPE                                         1   298
D59V13, multiclass
                                           clus
vv                                          DEL PEAK 20(6Q26) MUTATED
  ASIAN                                                            34
  BLACK OR AFRICAN AMERICAN                                         5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            87
                                           clus
vv                                          DEL PEAK 20(6Q26) WILD-TYPE
  ASIAN                                                              95
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             298
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED     2  90
  DEL PEAK 20(6Q26) WILD-TYPE   5 304
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED      2   90
  DEL PEAK 20(6Q26) WILD-TYPE    5  304
                        clus
vv                       DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           5
  NOT HISPANIC OR LATINO                        90                         304
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 21(7Q31.1) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q31.1) MUTATED    72  48
  DEL PEAK 21(7Q31.1) WILD-TYPE 282 173
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          120                           455 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                           48                           173 
$`DEL PEAK 21(7Q31.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78        14.30         7.63         5.92         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       32.45         7.69         0.85         2.63        20.12         3.88 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C 
       17.03         0.79         9.96         4.67        42.77         3.16 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V 
        3.68        47.93         3.16        29.00         6.94         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         0.36        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49R 
       16.47        13.55         8.71        10.36        12.43         0.10 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MR 
       13.25         0.10        12.46        12.76         0.10        13.22 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RB 
        0.13        33.11         5.06        15.78         2.89         5.29 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
        4.44        22.82         1.55        15.06         9.17        15.91 
TCGA-Z6-AAPN TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-8360 TCGA-BR-8361 
        2.66        26.10        18.05        28.73         6.18        19.50 
TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-BR-A4QI 
       14.04        11.54         7.53         1.48         1.15        13.64 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CG-4301 
        0.07         0.07         3.42         9.34        11.31         3.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 
        8.05        54.08        19.07        12.03        12.00        22.98 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A4YX TCGA-D7-A6EX TCGA-F1-6875 
       15.98        11.31        18.21        15.16        11.31        72.23 
TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
       19.53         0.56        22.75        11.77         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 
       23.84         9.67         8.88        27.42        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7BT 
       18.38        13.08         7.82         2.53        37.64         8.61 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       37.91         8.94        35.61         5.46        13.02        18.48 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A928 
       32.48         7.73        13.35        20.81         2.01         5.72 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       22.09        40.08        17.13        54.12        26.04        16.14 

$`DEL PEAK 21(7Q31.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        58.55        13.94        16.24         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 
       20.09        20.78        18.64         9.30         0.53        23.41 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
       12.82        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 
       60.39        68.02         3.68        41.52        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
        0.30         4.31         8.94        24.00         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88Z 
       58.59         4.90         7.13         7.43         8.71         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.95         3.02        35.97        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U 
        5.92        10.45        12.66        13.41        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        12.59        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.00        12.23        12.03        13.18         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
       53.95         9.30         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         3.42         4.80        15.35         9.27        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.18        42.87        46.19        11.24        10.16         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.10        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         6.08        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
       19.36        13.51         0.46        20.65        20.42        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-A48A 
        0.10         0.10         0.13         0.13         0.10        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         7.99         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        21.99         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-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        69.04        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        14.66        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-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ 
       12.30        11.84        24.20         3.25        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
        2.10        19.36        12.30         8.81        21.21         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19         1.41         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         5.56         1.81        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       20.15         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       28.96        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        18.74        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O 
        9.04        55.43         4.54         6.58        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11        12.43        10.62         0.79 

  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                        72.23                        122.30 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                       12.015                        12.820 
[1] "0.1 - 72.2 (12.0)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D60V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q31.1) MUTATED         1        5        4        8        18
  DEL PEAK 21(7Q31.1) WILD-TYPE      10       14       44       24        59
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q31.1) MUTATED          21        15         21          9
  DEL PEAK 21(7Q31.1) WILD-TYPE        63        14         76         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(7Q31.1) MUTATED            6        8         2
  DEL PEAK 21(7Q31.1) WILD-TYPE         42       43         2
D60V3, multiclass
            clus
vv           DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  STAGE I                              1                            10
  STAGE IA                             5                            14
  STAGE IB                             4                            44
  STAGE II                             8                            24
  STAGE IIA                           18                            59
  STAGE IIB                           21                            63
  STAGE III                           15                            14
  STAGE IIIA                          21                            76
  STAGE IIIB                           9                            63
  STAGE IIIC                           6                            42
  STAGE IV                             8                            43
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 21(7Q31.1) MUTATED      14  22  70  14
  DEL PEAK 21(7Q31.1) WILD-TYPE    39 104 210 110
D60V4, multiclass
       clus
vv      DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  T0+T1                          14                            39
  T2                             22                           104
  T3                             70                           210
  T4                             14                           110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 21(7Q31.1) MUTATED    36  51  20  13
  DEL PEAK 21(7Q31.1) WILD-TYPE 164 131  76  84
D60V5, multiclass
    clus
vv   DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  N0                          36                           164
  N1                          51                           131
  N2                          20                            76
  N3                          13                            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED   105   5
  DEL PEAK 21(7Q31.1) WILD-TYPE 408  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED    105    5
  DEL PEAK 21(7Q31.1) WILD-TYPE  408   34
   clus
vv  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  0                         105                           408
  1                           5                            34
[1] 2 2
[1] FALSE
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED    23 102
  DEL PEAK 21(7Q31.1) WILD-TYPE 159 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED     23  102
  DEL PEAK 21(7Q31.1) WILD-TYPE  159  325
        clus
vv       DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  FEMALE                          23                           159
  MALE                           102                           325
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 21(7Q31.1) MUTATED                                       6
  DEL PEAK 21(7Q31.1) WILD-TYPE                                    65
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q31.1) MUTATED                                                       23
  DEL PEAK 21(7Q31.1) WILD-TYPE                                                    139
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q31.1) MUTATED                                                                  15
  DEL PEAK 21(7Q31.1) WILD-TYPE                                                                66
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 21(7Q31.1) MUTATED                                                 18
  DEL PEAK 21(7Q31.1) WILD-TYPE                                               60
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 21(7Q31.1) MUTATED                                                          3
  DEL PEAK 21(7Q31.1) WILD-TYPE                                                       18
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 21(7Q31.1) MUTATED                                                           1
  DEL PEAK 21(7Q31.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 21(7Q31.1) MUTATED                                          2
  DEL PEAK 21(7Q31.1) WILD-TYPE                                       11
D60V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 21(7Q31.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 21(7Q31.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        65
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED     1 124
  DEL PEAK 21(7Q31.1) WILD-TYPE   5 479
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED      1  124
  DEL PEAK 21(7Q31.1) WILD-TYPE    5  479
     clus
vv    DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  NO                            1                             5
  YES                         124                           479
[1] 2 2
[1] FALSE
D60V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q31.1) MUTATED    62   1   3   2
  DEL PEAK 21(7Q31.1) WILD-TYPE 285  17  16  23
D60V11, multiclass
    clus
vv   DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  R0                          62                           285
  R1                           1                            17
  R2                           3                            16
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(7Q31.1) MUTATED      27                         3
  DEL PEAK 21(7Q31.1) WILD-TYPE   102                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(7Q31.1) MUTATED                                           1    73
  DEL PEAK 21(7Q31.1) WILD-TYPE                                         0   312
D60V13, multiclass
                                           clus
vv                                          DEL PEAK 21(7Q31.1) MUTATED
  ASIAN                                                              27
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              73
                                           clus
vv                                          DEL PEAK 21(7Q31.1) WILD-TYPE
  ASIAN                                                               102
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED     1  69
  DEL PEAK 21(7Q31.1) WILD-TYPE   6 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED      1   69
  DEL PEAK 21(7Q31.1) WILD-TYPE    6  325
                        clus
vv                       DEL PEAK 21(7Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK 21(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           325
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 22(7Q36.3) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(7Q36.3) MUTATED    96  61
  DEL PEAK 22(7Q36.3) WILD-TYPE 258 160
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          157                           418 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                           61                           160 
$`DEL PEAK 22(7Q36.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        14.30         7.63         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D 
        4.21         7.69         0.85        20.12        18.64        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        0.79         9.96        14.50        44.75        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON 
       42.77        25.22         3.16         3.68        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        7.17         3.16        58.59        29.00         7.13         6.94 
TCGA-L5-A88Y TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
        0.36        55.50         2.66        12.92        13.48        13.55 
TCGA-L5-A8NR TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        8.71        10.36        10.45        13.41         0.10        13.15 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
        0.10        12.46        12.59        12.76         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG 
       13.22        25.25        33.11         7.82         5.06        29.59 
TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
       15.78         5.29         4.44        18.81        12.43         1.55 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06        11.24         9.17        15.91         3.42         2.66 
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 
       19.56         9.44        17.29        19.33        26.10        35.24 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8369 
       28.73         3.45        11.44         0.69        15.58        14.04 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-8524 
        9.21        11.54         1.48         1.15         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.07         0.10         0.13         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 
       11.31        11.61         3.02         8.05        54.08        19.07 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 
       12.03        12.00        22.98        12.03        20.55        13.35 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 
       17.19        15.98        12.79        10.55        11.31        18.21 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-FP-7829 
       11.24        11.31         2.96         7.40        16.24        19.53 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
        0.56         5.92        22.75        11.77         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       23.84         9.67        27.42         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
       18.38         5.36        13.08         6.44         6.74         5.56 
TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-RD-A8N9 
        7.82        37.64        45.67        18.21        37.91        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ 
        5.46        13.02        18.48        32.48         7.73         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A92D 
       17.85        13.35        18.74        20.81         5.72        64.18 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       22.09        18.41        40.08        54.12        26.04        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 22(7Q36.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 
       31.27        58.55        13.94        32.45         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.09        20.78         2.63         3.88         9.30         0.53 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
       23.41        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       60.39        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M 
       24.03         6.28        30.25         0.30         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.00         4.70        32.61        19.99        21.01         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        1.38         4.90         7.43         8.71         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.40         3.95         3.02        35.97        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49U 
       52.57        46.09         5.92        12.66        12.43        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
        0.10        13.25        12.49        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
       11.54         4.47        12.33        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        13.18         0.13         5.16         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       14.70         7.04         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC 
        1.45        12.69         7.00        20.02        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU 
        4.80        15.35         9.27        19.96        22.82        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        30.71        18.18        42.87        46.19 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ 
       10.16         2.10        19.73        26.70        11.70        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         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-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       15.42        28.01        18.15        15.32        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49        14.43        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         8.05         0.56        12.95         2.66        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         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-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-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.07         0.07         0.07         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         0.13         0.10        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4460 
        7.99         4.01        14.01        29.98        47.05        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97         7.07        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        10.26        15.22 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.78        14.76        13.71        11.44         9.76        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        59.54         5.03        13.58         5.52         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-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-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        19.36        12.30         8.88         8.81        21.21 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1X 
        5.19         1.41        12.59         6.51         1.81        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        9.86         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79        13.25        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        34.45        27.88        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       65.16        36.69        11.70        11.93        61.22        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O 
        9.04         2.01        55.43         4.54         6.58        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        2.66        42.54        11.24        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        21.11        12.43        10.62 

  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                        68.02                        122.30 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                        12.33                         12.82 
[1] "0.1 - 68.0 (12.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D61V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(7Q36.3) MUTATED         1        5        6        9        20
  DEL PEAK 22(7Q36.3) WILD-TYPE      10       14       42       23        57
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(7Q36.3) MUTATED          32        15         27         13
  DEL PEAK 22(7Q36.3) WILD-TYPE        52        14         70         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(7Q36.3) MUTATED           11       13         3
  DEL PEAK 22(7Q36.3) WILD-TYPE         37       38         1
D61V3, multiclass
            clus
vv           DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  STAGE I                              1                            10
  STAGE IA                             5                            14
  STAGE IB                             6                            42
  STAGE II                             9                            23
  STAGE IIA                           20                            57
  STAGE IIB                           32                            52
  STAGE III                           15                            14
  STAGE IIIA                          27                            70
  STAGE IIIB                          13                            59
  STAGE IIIC                          11                            37
  STAGE IV                            13                            38
  STAGE IVA                            3                             1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 22(7Q36.3) MUTATED      17  31  85  24
  DEL PEAK 22(7Q36.3) WILD-TYPE    36  95 195 100
D61V4, multiclass
       clus
vv      DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  T0+T1                          17                            36
  T2                             31                            95
  T3                             85                           195
  T4                             24                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 22(7Q36.3) MUTATED    46  60  25  24
  DEL PEAK 22(7Q36.3) WILD-TYPE 154 122  71  73
D61V5, multiclass
    clus
vv   DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  N0                          46                           154
  N1                          60                           122
  N2                          25                            71
  N3                          24                            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"
D61V6, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED   134  12
  DEL PEAK 22(7Q36.3) WILD-TYPE 379  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED    134   12
  DEL PEAK 22(7Q36.3) WILD-TYPE  379   27
   clus
vv  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  0                         134                           379
  1                          12                            27
[1] 2 2
[1] FALSE
D61V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED    42 120
  DEL PEAK 22(7Q36.3) WILD-TYPE 140 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED     42  120
  DEL PEAK 22(7Q36.3) WILD-TYPE  140  307
        clus
vv       DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  FEMALE                          42                           140
  MALE                           120                           307
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 22(7Q36.3) MUTATED                                      12
  DEL PEAK 22(7Q36.3) WILD-TYPE                                    59
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(7Q36.3) MUTATED                                                       33
  DEL PEAK 22(7Q36.3) WILD-TYPE                                                    129
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(7Q36.3) MUTATED                                                                  17
  DEL PEAK 22(7Q36.3) WILD-TYPE                                                                64
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 22(7Q36.3) MUTATED                                                 24
  DEL PEAK 22(7Q36.3) WILD-TYPE                                               54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 22(7Q36.3) MUTATED                                                          5
  DEL PEAK 22(7Q36.3) WILD-TYPE                                                       16
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 22(7Q36.3) MUTATED                                                           1
  DEL PEAK 22(7Q36.3) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 22(7Q36.3) MUTATED                                          2
  DEL PEAK 22(7Q36.3) WILD-TYPE                                       11
D61V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 22(7Q36.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    2
                                                                   clus
vv                                                                  DEL PEAK 22(7Q36.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED     3 159
  DEL PEAK 22(7Q36.3) WILD-TYPE   3 444
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED      3  159
  DEL PEAK 22(7Q36.3) WILD-TYPE    3  444
     clus
vv    DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  NO                            3                             3
  YES                         159                           444
[1] 2 2
[1] FALSE
D61V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(7Q36.3) MUTATED    80   1   4   2
  DEL PEAK 22(7Q36.3) WILD-TYPE 267  17  15  23
D61V11, multiclass
    clus
vv   DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  R0                          80                           267
  R1                           1                            17
  R2                           4                            15
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(7Q36.3) MUTATED      36                         2
  DEL PEAK 22(7Q36.3) WILD-TYPE    93                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(7Q36.3) MUTATED                                           0    99
  DEL PEAK 22(7Q36.3) WILD-TYPE                                         1   286
D61V13, multiclass
                                           clus
vv                                          DEL PEAK 22(7Q36.3) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              99
                                           clus
vv                                          DEL PEAK 22(7Q36.3) WILD-TYPE
  ASIAN                                                                93
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED     2  95
  DEL PEAK 22(7Q36.3) WILD-TYPE   5 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED      2   95
  DEL PEAK 22(7Q36.3) WILD-TYPE    5  299
                        clus
vv                       DEL PEAK 22(7Q36.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK 22(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           299
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 23(8P23.2) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(8P23.2) MUTATED   117  74
  DEL PEAK 23(8P23.2) WILD-TYPE 237 147
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          191                           384 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                           74                           147 
$`DEL PEAK 23(8P23.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3Y9 
       25.78        31.27         5.92        13.94         4.21         0.85 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        18.64         3.88         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE 
       23.41         9.96        14.50        44.75        60.39         3.68 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        23.18        31.56        25.22        24.03 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT 
        4.31        24.00         3.68        32.61         3.32         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NL 
        7.43         2.60         7.40         3.95         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L7-A6VZ TCGA-LN-A49L 
        5.49         8.71        13.41        27.12        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.66        12.43        13.15        13.25        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.49        12.76        22.39        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       25.25        12.00         0.13         5.16         7.82         8.02 
TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       53.95         1.45        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       15.35         9.27        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       30.71        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 
        2.10         2.66        19.56         9.44        18.35        17.29 
TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 
       13.68         9.17        25.61        12.16         9.21        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       28.01        28.73        12.76         0.69         9.60        12.95 
TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-8682 
        2.66        15.58        13.08         9.21        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.86         8.22        13.87        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         3.42        12.43        11.61        12.20 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        3.02         7.99        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       19.07        22.98        36.00        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 
       69.04        12.66        19.13        18.54        17.19        15.22 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       11.31        24.72        16.44        15.65         7.40         0.62 
TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GD 
       17.06         5.92        12.59        14.17         0.76        22.75 
TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        6.25        27.42         3.39         1.41         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-R5-A7O7 
        6.51         1.81         7.82         2.53         5.56        45.67 
TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-SW-A7EB 
        8.52         9.24         8.61       122.30        37.91         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92        18.48        35.24        34.45         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A 
       22.19        12.79        17.85         1.87        13.35        36.69 
TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        1.71        52.24         4.54        11.24        18.41        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        54.12        16.14        21.11        12.43 

$`DEL PEAK 23(8P23.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR 
       14.30        58.55         7.63         8.94        16.24        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69         6.21        33.27        20.09        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 
        9.30        12.82        14.86         4.67        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       68.02        41.52        21.70         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        0.30         8.94         4.70        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       18.35         7.17         1.38         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A893 
        7.13         6.94         8.71        25.12         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50        35.97        12.92        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
        7.76        21.37        83.24        52.57        46.09         5.92 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A4 
       13.41         0.10        15.35         0.10         0.10        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
        0.10        15.52        11.54         4.47        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.03        13.18        33.11         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        29.59         6.35         9.30        15.78         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69         7.00        20.02         4.44        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JD 
       22.82         1.55        18.18        46.19        10.16         3.42 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
       19.73        26.70        11.70        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        6.97         4.64         7.43        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 
       26.10        32.78        18.05        19.89         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       30.90        31.20        32.94        12.82        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       23.93        18.15        15.32        12.43         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       18.71        17.49        14.43        11.44        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        16.31         2.20         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        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        0.26        15.85         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
        7.53         0.49        11.54        15.68        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-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         9.34 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
       11.31         6.58         0.10        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
       15.95         1.02         8.05        14.01        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07        65.10        21.07         7.99        12.36 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 
       10.26        15.98        12.79        10.55        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44         9.76         2.96         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         7.99        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47         1.51        14.27        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-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        23.84        12.30         9.67         8.88         8.81 
TCGA-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-A6RS TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
       13.08        12.59         5.56        13.51        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       37.64         3.72        19.73         9.86        18.21        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        6.08         4.60        11.05         5.13        16.67        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        27.88        32.48        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         2.70         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       27.35        64.57        14.33        65.16        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        20.81        22.68        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U 
        5.72        64.18        21.04         2.66        42.54        22.09 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        32.94        17.13        26.04        10.62         0.79 

  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                        122.3                         122.1 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                        12.59                         12.82 
[1] "0.1 - 122.3 (12.6)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1.1"
D62V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(8P23.2) MUTATED         3        4        8        8        25
  DEL PEAK 23(8P23.2) WILD-TYPE       8       15       40       24        52
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(8P23.2) MUTATED          32        13         29         30
  DEL PEAK 23(8P23.2) WILD-TYPE        52        16         68         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(8P23.2) MUTATED           17       19         2
  DEL PEAK 23(8P23.2) WILD-TYPE         31       32         2
D62V3, multiclass
            clus
vv           DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                             4                            15
  STAGE IB                             8                            40
  STAGE II                             8                            24
  STAGE IIA                           25                            52
  STAGE IIB                           32                            52
  STAGE III                           13                            16
  STAGE IIIA                          29                            68
  STAGE IIIB                          30                            42
  STAGE IIIC                          17                            31
  STAGE IV                            19                            32
  STAGE IVA                            2                             2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 23(8P23.2) MUTATED      18  35 108  32
  DEL PEAK 23(8P23.2) WILD-TYPE    35  91 172  92
D62V4, multiclass
       clus
vv      DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  T0+T1                          18                            35
  T2                             35                            91
  T3                            108                           172
  T4                             32                            92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 23(8P23.2) MUTATED    56  63  34  38
  DEL PEAK 23(8P23.2) WILD-TYPE 144 119  62  59
D62V5, multiclass
    clus
vv   DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  N0                          56                           144
  N1                          63                           119
  N2                          34                            62
  N3                          38                            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"
D62V6, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED   168  16
  DEL PEAK 23(8P23.2) WILD-TYPE 345  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED    168   16
  DEL PEAK 23(8P23.2) WILD-TYPE  345   23
   clus
vv  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  0                         168                           345
  1                          16                            23
[1] 2 2
[1] FALSE
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED    40 160
  DEL PEAK 23(8P23.2) WILD-TYPE 142 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED     40  160
  DEL PEAK 23(8P23.2) WILD-TYPE  142  267
        clus
vv       DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  FEMALE                          40                           142
  MALE                           160                           267
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 23(8P23.2) MUTATED                                       8
  DEL PEAK 23(8P23.2) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(8P23.2) MUTATED                                                       46
  DEL PEAK 23(8P23.2) WILD-TYPE                                                    116
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(8P23.2) MUTATED                                                                  27
  DEL PEAK 23(8P23.2) WILD-TYPE                                                                54
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 23(8P23.2) MUTATED                                                 26
  DEL PEAK 23(8P23.2) WILD-TYPE                                               52
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 23(8P23.2) MUTATED                                                          6
  DEL PEAK 23(8P23.2) WILD-TYPE                                                       15
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 23(8P23.2) MUTATED                                                           2
  DEL PEAK 23(8P23.2) WILD-TYPE                                                         6
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 23(8P23.2) MUTATED                                          3
  DEL PEAK 23(8P23.2) WILD-TYPE                                       10
D62V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 23(8P23.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 23(8P23.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED     2 198
  DEL PEAK 23(8P23.2) WILD-TYPE   4 405
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED      2  198
  DEL PEAK 23(8P23.2) WILD-TYPE    4  405
     clus
vv    DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  NO                            2                             4
  YES                         198                           405
[1] 2 2
[1] FALSE
D62V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 23(8P23.2) MUTATED    92   7   7   3
  DEL PEAK 23(8P23.2) WILD-TYPE 255  11  12  22
D62V11, multiclass
    clus
vv   DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  R0                          92                           255
  R1                           7                            11
  R2                           7                            12
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(8P23.2) MUTATED      47                         6
  DEL PEAK 23(8P23.2) WILD-TYPE    82                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 23(8P23.2) MUTATED                                           1   118
  DEL PEAK 23(8P23.2) WILD-TYPE                                         0   267
D62V13, multiclass
                                           clus
vv                                          DEL PEAK 23(8P23.2) MUTATED
  ASIAN                                                              47
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             118
                                           clus
vv                                          DEL PEAK 23(8P23.2) WILD-TYPE
  ASIAN                                                                82
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               267
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED     2 117
  DEL PEAK 23(8P23.2) WILD-TYPE   5 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED      2  117
  DEL PEAK 23(8P23.2) WILD-TYPE    5  277
                        clus
vv                       DEL PEAK 23(8P23.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         117
                        clus
vv                       DEL PEAK 23(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           277
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 24(9P23) MUTATION ANALYSIS
D63V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 24(9P23) MUTATED   170 106
  DEL PEAK 24(9P23) WILD-TYPE 184 115
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        276                         299 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        106                         115 
$`DEL PEAK 24(9P23) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         4.21        32.45         7.69        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H 
        3.88         0.53         0.79        23.41         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A938 TCGA-JY-A93E 
       12.16        44.75        60.39        68.02        25.41        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON 
        3.16         0.30         8.94         3.68        32.61        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         3.16        58.59         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        6.94         2.60         3.95        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L 
       16.47        13.22         8.71        13.41        83.24        10.45 
TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       12.66         0.10        15.35        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.59        12.49        12.76        22.39         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6KZ 
       12.23        12.03         0.13        33.11         5.16         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35         9.30        15.78         1.45        12.69 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       20.02        20.38         5.29         3.42         4.80         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR 
       18.31         8.12        28.11        42.87        46.19        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.44         6.61        18.35        17.29        13.68        19.33 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       19.89        12.16        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        18.15        15.32        28.73         3.45        18.71 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 
       17.49        11.44         0.69         8.05         2.66        16.31 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       22.19        17.52        14.04         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       20.22         7.53        16.44         9.86        15.68         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
       13.87        22.26         1.48         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-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 
        3.42        12.43        11.61         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        36.00         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 
       69.04        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        18.21        14.66        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 
        7.99        11.38        19.53        14.07        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GF TCGA-HU-A4GH 
        5.52         1.51         5.92        12.59        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        6.25        19.36         9.67        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51         5.56         7.82        13.51         5.56 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        45.67         8.52         6.08         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        5.13        16.67       122.30        37.91       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.79        48.79        13.25        18.48        35.24        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q 
        1.87        27.35        64.57        14.33        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71        36.16         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
        2.01        21.04        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       40.08        32.94        54.12        21.11        12.43         0.79 

$`DEL PEAK 24(9P23) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       58.55         5.92         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         2.63         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       14.86       122.10         3.68        41.52        42.77        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       23.18        31.56        24.03         6.28        30.25         4.31 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ 
       24.00         4.70        19.99        21.01        47.93         1.38 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        4.90        29.00         8.71        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
       21.37        27.12        52.57        46.09        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A4 TCGA-LN-A4A9 
       12.43        13.41        13.15         0.10        12.59        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
        4.47        13.18         7.82         8.02         7.59        14.70 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EY 
        7.04        53.95         2.89         7.00        15.35        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       18.18        15.06        11.24         9.17        15.91         2.10 
TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.70         9.47         6.97         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        21.11        30.90        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 
       23.93        12.43         9.07        12.76        14.43        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        9.60        20.55         0.56        12.95         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        19.50        13.08         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34        13.45         6.28         0.49        11.54        15.81 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         7.53         6.08        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        20.42        11.57         5.13         2.83        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 
        0.30         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         9.34        11.31         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02        27.02        15.95         1.02         7.99 
TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 
       14.01        21.99         0.00         9.01         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5725 
       30.97         6.97         0.99         6.02         0.99        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 
       28.96        79.07        65.10        21.07         7.99        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        15.22        10.55        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       17.19        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       14.76        13.71        11.44         9.76         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62        16.24        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
        3.48        22.29        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47        14.27        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       23.84        12.30         8.88         8.81         3.45         3.39 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
       13.08         1.81         2.53        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         9.86        18.21        61.25         4.60        11.05 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       19.04         0.92         5.46        13.02        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO 
       32.48        28.96        34.29        46.26        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        13.35        26.24        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 
       11.70        11.93        61.22        22.68         7.36        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 
        4.54         6.58         5.72        64.18         2.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       29.98        17.13        26.04        16.14        10.62 

  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                       0.07                        0.00 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                      122.3                       122.1 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                     12.625                      12.820 
[1] "0.1 - 122.3 (12.6)" "0.0 - 122.1 (12.8)"
[1] "hr=" "1"  
D63V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P23) MUTATED         3        9       15       17        41
  DEL PEAK 24(9P23) WILD-TYPE       8       10       33       15        36
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P23) MUTATED          41        19         46         35
  DEL PEAK 24(9P23) WILD-TYPE        43        10         51         37
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(9P23) MUTATED           19       23         4
  DEL PEAK 24(9P23) WILD-TYPE         29       28         0
D63V3, multiclass
            clus
vv           DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  STAGE I                            3                           8
  STAGE IA                           9                          10
  STAGE IB                          15                          33
  STAGE II                          17                          15
  STAGE IIA                         41                          36
  STAGE IIB                         41                          43
  STAGE III                         19                          10
  STAGE IIIA                        46                          51
  STAGE IIIB                        35                          37
  STAGE IIIC                        19                          29
  STAGE IV                          23                          28
  STAGE IVA                          4                           0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  DEL PEAK 24(9P23) MUTATED      26  59 146  46
  DEL PEAK 24(9P23) WILD-TYPE    27  67 134  78
D63V4, multiclass
       clus
vv      DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  T0+T1                        26                          27
  T2                           59                          67
  T3                          146                         134
  T4                           46                          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 24(9P23) MUTATED    86  97  48  43
  DEL PEAK 24(9P23) WILD-TYPE 114  85  48  54
D63V5, multiclass
    clus
vv   DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  N0                        86                         114
  N1                        97                          85
  N2                        48                          48
  N3                        43                          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"
D63V6, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED   248  16
  DEL PEAK 24(9P23) WILD-TYPE 265  23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED    248   16
  DEL PEAK 24(9P23) WILD-TYPE  265   23
   clus
vv  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  0                       248                         265
  1                        16                          23
[1] 2 2
[1] FALSE
D63V7, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED    75 217
  DEL PEAK 24(9P23) WILD-TYPE 107 210
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED     75  217
  DEL PEAK 24(9P23) WILD-TYPE  107  210
        clus
vv       DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  FEMALE                        75                         107
  MALE                         217                         210
[1] 2 2
[1] FALSE
                             vv
clus                          STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 24(9P23) MUTATED                                      22
  DEL PEAK 24(9P23) WILD-TYPE                                    49
                             vv
clus                          STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P23) MUTATED                                                       67
  DEL PEAK 24(9P23) WILD-TYPE                                                     95
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P23) MUTATED                                                                  43
  DEL PEAK 24(9P23) WILD-TYPE                                                                38
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 24(9P23) MUTATED                                                 42
  DEL PEAK 24(9P23) WILD-TYPE                                               36
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 24(9P23) MUTATED                                                          9
  DEL PEAK 24(9P23) WILD-TYPE                                                       12
                             vv
clus                          STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 24(9P23) MUTATED                                                           3
  DEL PEAK 24(9P23) WILD-TYPE                                                         5
                             vv
clus                          STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 24(9P23) MUTATED                                          4
  DEL PEAK 24(9P23) WILD-TYPE                                        9
D63V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 24(9P23) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                    22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                   67
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                        43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                         42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                  9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                 3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                  4
                                                                   clus
vv                                                                  DEL PEAK 24(9P23) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED     3 289
  DEL PEAK 24(9P23) WILD-TYPE   3 314
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED      3  289
  DEL PEAK 24(9P23) WILD-TYPE    3  314
     clus
vv    DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  NO                          3                           3
  YES                       289                         314
[1] 2 2
[1] FALSE
D63V10, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 24(9P23) MUTATED   152   9   7   9
  DEL PEAK 24(9P23) WILD-TYPE 195   9  12  16
D63V11, multiclass
    clus
vv   DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  R0                       152                         195
  R1                         9                           9
  R2                         7                          12
  RX                         9                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(9P23) MUTATED      63                         6
  DEL PEAK 24(9P23) WILD-TYPE    66                         7
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 24(9P23) MUTATED                                           1   177
  DEL PEAK 24(9P23) WILD-TYPE                                         0   208
D63V13, multiclass
                                           clus
vv                                          DEL PEAK 24(9P23) MUTATED
  ASIAN                                                            63
  BLACK OR AFRICAN AMERICAN                                         6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           177
                                           clus
vv                                          DEL PEAK 24(9P23) WILD-TYPE
  ASIAN                                                              66
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED     4 184
  DEL PEAK 24(9P23) WILD-TYPE   3 210
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED      4  184
  DEL PEAK 24(9P23) WILD-TYPE    3  210
                        clus
vv                       DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       184                         210
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 25(9P21.3) MUTATION ANALYSIS
D64V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 25(9P21.3) MUTATED   189 119
  DEL PEAK 25(9P21.3) WILD-TYPE 165 102
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          308                           267 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          119                           102 
$`DEL PEAK 25(9P21.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        14.30         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12        18.64         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       12.16        44.75        60.39        25.41        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
        3.16         0.30         4.31         8.94         3.68        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93        18.35         3.32         7.17        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
       29.00         7.13         7.43         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.41        83.24        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.03        13.18         0.13        33.11         5.16         7.82 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        14.70        29.59         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        1.45        12.69        20.02        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D 
        1.55        18.31         8.12        28.11        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.10         2.66        19.73        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6709 
        6.61        18.35        17.29        13.68        19.33        12.16 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       31.20         9.21        35.24        15.42        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32        28.73         3.45        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
       11.44         0.69        16.31        22.19        17.52        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8682 
        5.39        25.18         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 
        9.86        15.68         8.22        13.87        22.26         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-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 
        3.42        12.43        11.61         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        36.00         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        69.04        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        18.21        14.66        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 
        7.99        72.23        11.38        17.06        13.58         0.56 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-A4G3 TCGA-HU-A4GH 
        1.51         5.92        14.27        12.59         5.59        11.77 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        6.25        12.30         9.67        27.42        21.21        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.36         5.19         1.41         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        45.67         8.52         6.08         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
        5.13        16.67        37.91       115.69         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79        13.25        13.02        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       34.45        32.48         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70        17.85         1.87        27.35        64.57        14.33 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81         1.71        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       52.24         9.04        21.04        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K 
       18.41        40.08        32.94        54.12        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

$`DEL PEAK 25(9P21.3) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A4QT 
       58.55         5.92        13.94         6.21        20.09         9.30 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.86       122.10        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OE 
       21.70        31.56        24.03         6.28        30.25        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88T 
        4.70        19.99        21.01         1.38         3.16         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NT TCGA-L5-A8NV 
       25.12         7.40        13.48         7.76        27.12        52.57 
TCGA-L5-A8NW TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6Y0 
       46.09         0.10         8.02         7.59         7.04        53.95 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EY TCGA-VR-A8Q7 
        2.89         7.00        15.35        19.96        30.71        42.87 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       18.05        19.89         8.98        21.11        30.90        32.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       12.82        24.76        23.93        12.43         9.07        12.76 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       13.08         0.26         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        7.53        11.54        15.81        10.68        12.56         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53        12.82        19.36         0.46        11.57         5.13 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 
       13.18         0.30         0.10         0.13         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         9.34        11.31         6.58        12.20         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02        15.95         1.02         7.99         8.05 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 
       21.99         0.00         9.01         7.07        22.98         6.97 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.36        19.13        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.22        10.55        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        20.91         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       13.71        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         0.62        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF 
       19.53        14.07        22.29        59.54         5.03         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        0.23        18.08        26.47        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 
       19.36        23.84         8.88         8.81         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A93G TCGA-MX-A5UG 
       18.38        13.08         6.44         1.81        20.15         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         9.86        18.21        61.25         4.60        11.05 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 
       16.87        19.04         0.92         5.46        27.88        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        26.24        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       61.22        22.68         7.36         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B 
        6.58         5.72        64.18         2.66        28.41        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I 
       17.13        26.04        16.14 

  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                       115.69                        122.30 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                       12.625                        12.890 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (12.9)"
[1] "hr=" "1.1"
D64V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9P21.3) MUTATED         3       11       22       17        47
  DEL PEAK 25(9P21.3) WILD-TYPE       8        8       26       15        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9P21.3) MUTATED          44        23         48         36
  DEL PEAK 25(9P21.3) WILD-TYPE        40         6         49         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(9P21.3) MUTATED           18       27         4
  DEL PEAK 25(9P21.3) WILD-TYPE         30       24         0
D64V3, multiclass
            clus
vv           DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  STAGE I                              3                             8
  STAGE IA                            11                             8
  STAGE IB                            22                            26
  STAGE II                            17                            15
  STAGE IIA                           47                            30
  STAGE IIB                           44                            40
  STAGE III                           23                             6
  STAGE IIIA                          48                            49
  STAGE IIIB                          36                            36
  STAGE IIIC                          18                            30
  STAGE IV                            27                            24
  STAGE IVA                            4                             0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 25(9P21.3) MUTATED      29  70 159  47
  DEL PEAK 25(9P21.3) WILD-TYPE    24  56 121  77
D64V4, multiclass
       clus
vv      DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  T0+T1                          29                            24
  T2                             70                            56
  T3                            159                           121
  T4                             47                            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 25(9P21.3) MUTATED   107 103  52  41
  DEL PEAK 25(9P21.3) WILD-TYPE  93  79  44  56
D64V5, multiclass
    clus
vv   DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  N0                         107                            93
  N1                         103                            79
  N2                          52                            44
  N3                          41                            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"
D64V6, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED   266  20
  DEL PEAK 25(9P21.3) WILD-TYPE 247  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED    266   20
  DEL PEAK 25(9P21.3) WILD-TYPE  247   19
   clus
vv  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  0                         266                           247
  1                          20                            19
[1] 2 2
[1] FALSE
D64V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED    80 240
  DEL PEAK 25(9P21.3) WILD-TYPE 102 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED     80  240
  DEL PEAK 25(9P21.3) WILD-TYPE  102  187
        clus
vv       DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  FEMALE                          80                           102
  MALE                           240                           187
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 25(9P21.3) MUTATED                                      18
  DEL PEAK 25(9P21.3) WILD-TYPE                                    53
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9P21.3) MUTATED                                                       67
  DEL PEAK 25(9P21.3) WILD-TYPE                                                     95
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9P21.3) MUTATED                                                                  45
  DEL PEAK 25(9P21.3) WILD-TYPE                                                                36
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 25(9P21.3) MUTATED                                                 40
  DEL PEAK 25(9P21.3) WILD-TYPE                                               38
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 25(9P21.3) MUTATED                                                          9
  DEL PEAK 25(9P21.3) WILD-TYPE                                                       12
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 25(9P21.3) MUTATED                                                           4
  DEL PEAK 25(9P21.3) WILD-TYPE                                                         4
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 25(9P21.3) MUTATED                                          5
  DEL PEAK 25(9P21.3) WILD-TYPE                                        8
D64V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 25(9P21.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                      18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     67
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    5
                                                                   clus
vv                                                                  DEL PEAK 25(9P21.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       95
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            36
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED     3 317
  DEL PEAK 25(9P21.3) WILD-TYPE   3 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED      3  317
  DEL PEAK 25(9P21.3) WILD-TYPE    3  286
     clus
vv    DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  NO                            3                             3
  YES                         317                           286
[1] 2 2
[1] FALSE
D64V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 25(9P21.3) MUTATED   153   8   8   6
  DEL PEAK 25(9P21.3) WILD-TYPE 194  10  11  19
D64V11, multiclass
    clus
vv   DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  R0                         153                           194
  R1                           8                            10
  R2                           8                            11
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(9P21.3) MUTATED      73                         8
  DEL PEAK 25(9P21.3) WILD-TYPE    56                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 25(9P21.3) MUTATED                                           1   190
  DEL PEAK 25(9P21.3) WILD-TYPE                                         0   195
D64V13, multiclass
                                           clus
vv                                          DEL PEAK 25(9P21.3) MUTATED
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             190
                                           clus
vv                                          DEL PEAK 25(9P21.3) WILD-TYPE
  ASIAN                                                                56
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED     4 195
  DEL PEAK 25(9P21.3) WILD-TYPE   3 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED      4  195
  DEL PEAK 25(9P21.3) WILD-TYPE    3  199
                        clus
vv                       DEL PEAK 25(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       DEL PEAK 25(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           199
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 26(9Q21.11) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(9Q21.11) MUTATED    97  66
  DEL PEAK 26(9Q21.11) WILD-TYPE 257 155
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           163                            412 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                            66                            155 
$`DEL PEAK 26(9Q21.11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GO TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       25.78        31.27        16.24         0.85        20.78        20.12 
TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A93E 
        3.88         0.79        23.41         4.67        44.75        25.22 
TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW 
        0.30         8.94         3.68        47.93        58.59         7.13 
TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NS TCGA-L5-A8NW 
        6.94        55.50         2.66        35.97        13.41        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
        5.92        12.66         0.10        13.15        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.59        12.76         0.10        12.33        12.00        12.23 
TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        0.13         5.06        29.59         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP 
        1.45        12.69         3.42         4.80        18.81        19.96 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        1.55         8.12        28.11        18.18        42.87        11.24 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
       10.16         3.42         2.10        19.73        11.01         9.44 
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7715 
        6.61        17.29        13.68        19.33        31.20        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8286 
       28.01        18.15        28.73         3.45        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        17.52         5.39        25.18         9.21 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       16.44        15.68         8.22        22.26         1.48         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         3.42 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4438 TCGA-CG-4455 
       11.31        11.61        12.20        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        18.21        14.66        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         7.99        72.23        11.38        17.06        13.58 
TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GH 
        0.56         5.92        12.59        14.17        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RP 
        6.25         2.10         9.67        18.38         5.36         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF 
        6.74         6.51         7.82        37.64        45.67         8.52 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV 
        6.08        16.67        37.91         8.94         5.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        35.24        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A94O 
       13.35        20.81        36.16         9.73         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J 
       42.54        11.24        22.09        40.08        32.94        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 26(9Q21.11) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       14.30        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 
        2.63        18.64         9.30         0.53        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
        9.96        14.86        14.50        12.16       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
       29.00         7.43         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.95         3.02        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       27.12        83.24        52.57        10.36        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.41        15.35         0.10         0.10        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        10.52        12.03        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        7.82         8.02         7.59        14.70         7.04        53.95 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
        2.89         7.00        20.02        20.38         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY 
        9.27         4.44        22.82        12.43        18.31        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-B7-5816 
       46.19        15.06         9.17        15.91         2.66        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       15.95        13.87        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       23.93        15.32        12.43         9.07        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 
        6.18        19.50        13.08         0.26         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-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         9.34        13.45         6.28         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         9.86        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        7.53         6.08        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-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         9.34        12.43         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.66        11.93        19.13        18.61        17.85        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        19.50        17.19        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-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        0.62        16.24        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
       14.07        22.29        59.54         5.03         5.52         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47         1.51        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-A4GP 
       24.20         3.25        22.75        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        10.19         0.26        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45        18.81         3.39         5.19        13.08         1.41 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       60.56        20.15         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87        19.04         0.92        48.79         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        21.73        34.45        27.88        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM 
       28.96        34.29        46.26        16.31         2.50         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       18.74        22.68         1.71         7.36         9.50        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        2.01        55.43         4.54         6.58         5.72        64.18 
TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        18.41        28.41        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        12.43        10.62 

  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                         12.69                          12.79 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(9Q21.11) MUTATED         1        4       11       11        22
  DEL PEAK 26(9Q21.11) WILD-TYPE      10       15       37       21        55
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(9Q21.11) MUTATED          25         7         27         20
  DEL PEAK 26(9Q21.11) WILD-TYPE        59        22         70         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(9Q21.11) MUTATED           15       12         4
  DEL PEAK 26(9Q21.11) WILD-TYPE         33       39         0
D65V3, multiclass
            clus
vv           DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              4                             15
  STAGE IB                             11                             37
  STAGE II                             11                             21
  STAGE IIA                            22                             55
  STAGE IIB                            25                             59
  STAGE III                             7                             22
  STAGE IIIA                           27                             70
  STAGE IIIB                           20                             52
  STAGE IIIC                           15                             33
  STAGE IV                             12                             39
  STAGE IVA                             4                              0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 26(9Q21.11) MUTATED      12  30  88  31
  DEL PEAK 26(9Q21.11) WILD-TYPE    41  96 192  93
D65V4, multiclass
       clus
vv      DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  T0+T1                           12                             41
  T2                              30                             96
  T3                              88                            192
  T4                              31                             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 26(9Q21.11) MUTATED    53  51  30  25
  DEL PEAK 26(9Q21.11) WILD-TYPE 147 131  66  72
D65V5, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  N0                           53                            147
  N1                           51                            131
  N2                           30                             66
  N3                           25                             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"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED   143  10
  DEL PEAK 26(9Q21.11) WILD-TYPE 370  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED    143   10
  DEL PEAK 26(9Q21.11) WILD-TYPE  370   29
   clus
vv  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  0                          143                            370
  1                           10                             29
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED    42 129
  DEL PEAK 26(9Q21.11) WILD-TYPE 140 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED     42  129
  DEL PEAK 26(9Q21.11) WILD-TYPE  140  298
        clus
vv       DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  FEMALE                           42                            140
  MALE                            129                            298
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 26(9Q21.11) MUTATED                                      13
  DEL PEAK 26(9Q21.11) WILD-TYPE                                    58
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(9Q21.11) MUTATED                                                       46
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                    116
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(9Q21.11) MUTATED                                                                  19
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 26(9Q21.11) MUTATED                                                 26
  DEL PEAK 26(9Q21.11) WILD-TYPE                                               52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 26(9Q21.11) MUTATED                                                          5
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 26(9Q21.11) MUTATED                                                           3
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 26(9Q21.11) MUTATED                                          1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                       12
D65V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 26(9Q21.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 26(9Q21.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       116
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     1 170
  DEL PEAK 26(9Q21.11) WILD-TYPE   5 433
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      1  170
  DEL PEAK 26(9Q21.11) WILD-TYPE    5  433
     clus
vv    DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  NO                             1                              5
  YES                          170                            433
[1] 2 2
[1] FALSE
D65V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(9Q21.11) MUTATED    88   4   3   5
  DEL PEAK 26(9Q21.11) WILD-TYPE 259  14  16  20
D65V11, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  R0                           88                            259
  R1                            4                             14
  R2                            3                             16
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(9Q21.11) MUTATED      42                         7
  DEL PEAK 26(9Q21.11) WILD-TYPE    87                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(9Q21.11) MUTATED                                           0
  DEL PEAK 26(9Q21.11) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 26(9Q21.11) MUTATED     105
  DEL PEAK 26(9Q21.11) WILD-TYPE   280
D65V13, multiclass
                                           clus
vv                                          DEL PEAK 26(9Q21.11) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              105
                                           clus
vv                                          DEL PEAK 26(9Q21.11) WILD-TYPE
  ASIAN                                                                 87
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     3 116
  DEL PEAK 26(9Q21.11) WILD-TYPE   4 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      3  116
  DEL PEAK 26(9Q21.11) WILD-TYPE    4  278
                        clus
vv                       DEL PEAK 26(9Q21.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       DEL PEAK 26(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            278
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 27(10P15.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.3) MUTATED    63  55
  DEL PEAK 27(10P15.3) WILD-TYPE 291 166
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           118                            457 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                            55                            166 
$`DEL PEAK 27(10P15.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       25.78        14.30         5.92         4.21        33.27         0.85 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C 
       18.64         0.53         0.79        23.41        14.50        23.18 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OO 
        0.30         4.31         8.94        24.00         4.70         3.32 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        3.16         4.90         2.60        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        5.92        13.41        13.25        22.39        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22         4.47        25.25        12.03        13.18         0.13 
TCGA-Q9-A6FW TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EW 
        7.82        53.95         5.29         3.42         4.80         8.12 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TI 
       18.18        15.06        11.24         3.42         2.66        19.56 
TCGA-B7-A5TJ TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 
       11.01        18.35         6.18        19.33        26.10         3.45 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8678 
       14.43        11.44        16.31        17.52        20.22        11.54 
TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4IY TCGA-BR-A4J7 TCGA-CD-8525 TCGA-CD-8527 
        9.86         7.53        12.89        19.36         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4441 
        0.10         0.13         0.13         9.34         3.02        14.01 
TCGA-CG-4455 TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-6815 
       12.03        22.98        69.04        18.54        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-EQ-8122 
       11.31        24.72        18.21        14.27        11.24         7.99 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 
       19.53         0.56         5.52         0.23         5.92        14.17 
TCGA-HU-A4GU TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7ZF 
        6.25        18.81         1.41         6.44         6.74         8.52 
TCGA-R5-A805 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        9.24       115.69         8.94         5.79         0.92        48.79 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PS TCGA-VQ-A91N 
       13.02        18.48        35.24        32.48        13.35        18.74 
TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T 
       20.81         9.04         4.54         5.72        64.18        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       18.41        40.08        16.14         0.79 

$`DEL PEAK 27(10P15.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69         6.21        20.09        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        12.16       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       68.02         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.68        32.61        19.99        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        7.17         1.38        58.59        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        6.94         8.71        25.12         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       16.47        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
        8.71        52.57        46.09        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43         0.10        13.15        15.35         0.10         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-M9-A5M8 
       15.52        12.33        10.52        12.00        12.23        33.11 
TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       29.59         6.35         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00        20.02        20.38        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        4.44        18.81        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D 
       18.31        28.11        30.71        42.87        46.19         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       15.91        10.16         2.10        19.73        26.70        11.70 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       17.29        13.68        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        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        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       12.43         9.07        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         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        15.81        16.44        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56        13.87         6.08        22.26         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       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-8530 
       13.18         0.30         0.07         0.07         0.07         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-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-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       54.08         4.01        29.98        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-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        14.66        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-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-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-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        23.84        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-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19        13.08        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       61.25         6.08         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DV 
       57.44        35.61        16.87        19.04         5.46        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        9.50         9.73        52.24         2.01        55.43         6.58 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A 
       21.04         2.66        42.54        22.09        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        54.12        26.04        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                         11.54                          12.82 
[1] "0.1 - 115.7 (11.5)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.5"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10P15.3) MUTATED         1        3        6        3        14
  DEL PEAK 27(10P15.3) WILD-TYPE      10       16       42       29        63
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10P15.3) MUTATED          23        10         22         13
  DEL PEAK 27(10P15.3) WILD-TYPE        61        19         75         59
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 27(10P15.3) MUTATED            9       13         0
  DEL PEAK 27(10P15.3) WILD-TYPE         39       38         4
D66V3, multiclass
            clus
vv           DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              3                             16
  STAGE IB                              6                             42
  STAGE II                              3                             29
  STAGE IIA                            14                             63
  STAGE IIB                            23                             61
  STAGE III                            10                             19
  STAGE IIIA                           22                             75
  STAGE IIIB                           13                             59
  STAGE IIIC                            9                             39
  STAGE IV                             13                             38
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 27(10P15.3) MUTATED       7  27  64  21
  DEL PEAK 27(10P15.3) WILD-TYPE    46  99 216 103
D66V4, multiclass
       clus
vv      DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  T0+T1                            7                             46
  T2                              27                             99
  T3                              64                            216
  T4                              21                            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 27(10P15.3) MUTATED    33  38  26  20
  DEL PEAK 27(10P15.3) WILD-TYPE 167 144  70  77
D66V5, multiclass
    clus
vv   DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  N0                           33                            167
  N1                           38                            144
  N2                           26                             70
  N3                           20                             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"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED   106   7
  DEL PEAK 27(10P15.3) WILD-TYPE 407  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED    106    7
  DEL PEAK 27(10P15.3) WILD-TYPE  407   32
   clus
vv  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  0                          106                            407
  1                            7                             32
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED    29  96
  DEL PEAK 27(10P15.3) WILD-TYPE 153 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     29   96
  DEL PEAK 27(10P15.3) WILD-TYPE  153  331
        clus
vv       DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  FEMALE                           29                            153
  MALE                             96                            331
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 27(10P15.3) MUTATED                                       8
  DEL PEAK 27(10P15.3) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10P15.3) MUTATED                                                       22
  DEL PEAK 27(10P15.3) WILD-TYPE                                                    140
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10P15.3) MUTATED                                                                  14
  DEL PEAK 27(10P15.3) WILD-TYPE                                                                67
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 27(10P15.3) MUTATED                                                 21
  DEL PEAK 27(10P15.3) WILD-TYPE                                               57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 27(10P15.3) MUTATED                                                          7
  DEL PEAK 27(10P15.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 27(10P15.3) MUTATED                                                           1
  DEL PEAK 27(10P15.3) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 27(10P15.3) MUTATED                                          3
  DEL PEAK 27(10P15.3) WILD-TYPE                                       10
D66V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 27(10P15.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 27(10P15.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED     1 124
  DEL PEAK 27(10P15.3) WILD-TYPE   5 479
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED      1  124
  DEL PEAK 27(10P15.3) WILD-TYPE    5  479
     clus
vv    DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  NO                             1                              5
  YES                          124                            479
[1] 2 2
[1] FALSE
D66V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10P15.3) MUTATED    60   3   3   6
  DEL PEAK 27(10P15.3) WILD-TYPE 287  15  16  19
D66V11, multiclass
    clus
vv   DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  R0                           60                            287
  R1                            3                             15
  R2                            3                             16
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(10P15.3) MUTATED      32                         4
  DEL PEAK 27(10P15.3) WILD-TYPE    97                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(10P15.3) MUTATED                                           0
  DEL PEAK 27(10P15.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 27(10P15.3) MUTATED      72
  DEL PEAK 27(10P15.3) WILD-TYPE   313
D66V13, multiclass
                                           clus
vv                                          DEL PEAK 27(10P15.3) MUTATED
  ASIAN                                                               32
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               72
                                           clus
vv                                          DEL PEAK 27(10P15.3) WILD-TYPE
  ASIAN                                                                 97
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED     1  79
  DEL PEAK 27(10P15.3) WILD-TYPE   6 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED      1   79
  DEL PEAK 27(10P15.3) WILD-TYPE    6  315
                        clus
vv                       DEL PEAK 27(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 27(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            315
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 28(10P11.21) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10P11.21) MUTATED    48  41
  DEL PEAK 28(10P11.21) WILD-TYPE 306 180
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             89                             486 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             41                             180 
$`DEL PEAK 28(10P11.21) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC 
       14.30         5.92        13.94        33.27         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
       18.64         0.53         0.79        23.41        14.50        44.75 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
        3.68        23.18         0.30         4.31        24.00         4.70 
TCGA-L5-A4OT TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49O 
        4.90        13.48        13.55        27.12        83.24        13.41 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A9 
       13.15         0.10        13.25        12.59        22.39        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A9FO 
       13.22         4.47        25.25        10.52        13.18         0.13 
TCGA-V5-A7RC TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        3.42         8.12        28.11        18.18        15.06        11.24 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 
        3.42         2.66        19.33        26.10         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       11.44        16.31        17.52         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-A4MH TCGA-CG-4455 TCGA-CG-4475 TCGA-CG-5732 TCGA-D7-6521 
        0.13        12.20        12.03        22.98        69.04        18.54 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6F0 TCGA-FP-7829 
       15.98        12.79        11.31        18.21         2.96        19.53 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-8462 
        0.56         5.52        14.17        12.10        12.30        18.81 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-R5-A7ZF TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB 
        1.41         6.44         8.52       115.69         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PS TCGA-VQ-A91N 
       48.79        13.02        18.48        35.24        13.35        18.74 
TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       20.81         5.72        11.24        40.08         0.79 

$`DEL PEAK 28(10P11.21) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55         7.63         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YA 
        4.21        32.45         7.69         6.21        20.09        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        2.63         3.88         9.30        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        60.39        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         8.94         3.68 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       32.61        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38         3.16        58.59        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        7.40         3.95         3.02        55.50         2.66        35.97 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       12.92        16.47        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        46.09        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X 
       10.45        12.66        12.43         0.10        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.46        12.49        12.76        12.59         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 
       12.33        12.33        12.00        12.23        12.03        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        2.89         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         4.80        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        18.31        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE 
       42.87        46.19         9.17        15.91        10.16         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         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-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.87        17.29        13.68        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        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        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        15.68         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        22.26         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        3.42         9.34        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
       15.02        28.96        79.07        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.61        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.22        10.55        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44         9.76        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        7.40         7.13         0.62         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        8.88         8.81        27.42        21.21         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36         5.19        13.08         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        60.56        20.15        37.64         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        9.86        45.67        18.21        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E3 
       16.87        19.04         0.92         5.46        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       11.93        61.22        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        52.24         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58        64.18        21.04         2.66        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       22.09        18.41        28.41        32.94        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        21.11        12.43        10.62 

  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                         13.150                          12.675 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.3"
D67V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10P11.21) MUTATED         1        1        3        3        19
  DEL PEAK 28(10P11.21) WILD-TYPE      10       18       45       29        58
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10P11.21) MUTATED          17         7         17          7
  DEL PEAK 28(10P11.21) WILD-TYPE        67        22         80         65
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(10P11.21) MUTATED            5       10         1
  DEL PEAK 28(10P11.21) WILD-TYPE         43       41         3
D67V3, multiclass
            clus
vv           DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  STAGE I                                1                              10
  STAGE IA                               1                              18
  STAGE IB                               3                              45
  STAGE II                               3                              29
  STAGE IIA                             19                              58
  STAGE IIB                             17                              67
  STAGE III                              7                              22
  STAGE IIIA                            17                              80
  STAGE IIIB                             7                              65
  STAGE IIIC                             5                              43
  STAGE IV                              10                              41
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 28(10P11.21) MUTATED       5  25  52   9
  DEL PEAK 28(10P11.21) WILD-TYPE    48 101 228 115
D67V4, multiclass
       clus
vv      DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  T0+T1                             5                              48
  T2                               25                             101
  T3                               52                             228
  T4                                9                             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"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 28(10P11.21) MUTATED    30  28  18  14
  DEL PEAK 28(10P11.21) WILD-TYPE 170 154  78  83
D67V5, multiclass
    clus
vv   DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  N0                            30                             170
  N1                            28                             154
  N2                            18                              78
  N3                            14                              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"
D67V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    84   6
  DEL PEAK 28(10P11.21) WILD-TYPE 429  33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     84    6
  DEL PEAK 28(10P11.21) WILD-TYPE  429   33
   clus
vv  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  0                            84                             429
  1                             6                              33
[1] 2 2
[1] FALSE
D67V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    25  70
  DEL PEAK 28(10P11.21) WILD-TYPE 157 357
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     25   70
  DEL PEAK 28(10P11.21) WILD-TYPE  157  357
        clus
vv       DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  FEMALE                            25                             157
  MALE                              70                             357
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 28(10P11.21) MUTATED                                       5
  DEL PEAK 28(10P11.21) WILD-TYPE                                    66
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10P11.21) MUTATED                                                       14
  DEL PEAK 28(10P11.21) WILD-TYPE                                                    148
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10P11.21) MUTATED                                                                   9
  DEL PEAK 28(10P11.21) WILD-TYPE                                                                72
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 28(10P11.21) MUTATED                                                 12
  DEL PEAK 28(10P11.21) WILD-TYPE                                               66
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 28(10P11.21) MUTATED                                                          5
  DEL PEAK 28(10P11.21) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 28(10P11.21) MUTATED                                                           2
  DEL PEAK 28(10P11.21) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 28(10P11.21) MUTATED                                          2
  DEL PEAK 28(10P11.21) WILD-TYPE                                       11
D67V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 28(10P11.21) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  DEL PEAK 28(10P11.21) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              72
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED     2  93
  DEL PEAK 28(10P11.21) WILD-TYPE   4 510
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED      2   93
  DEL PEAK 28(10P11.21) WILD-TYPE    4  510
     clus
vv    DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  NO                              2                               4
  YES                            93                             510
[1] 2 2
[1] FALSE
D67V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10P11.21) MUTATED    41   3   1   3
  DEL PEAK 28(10P11.21) WILD-TYPE 306  15  18  22
D67V11, multiclass
    clus
vv   DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  R0                            41                             306
  R1                             3                              15
  R2                             1                              18
  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"
D67V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(10P11.21) MUTATED      29                         4
  DEL PEAK 28(10P11.21) WILD-TYPE   100                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(10P11.21) MUTATED                                           0
  DEL PEAK 28(10P11.21) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 28(10P11.21) MUTATED      50
  DEL PEAK 28(10P11.21) WILD-TYPE   335
D67V13, multiclass
                                           clus
vv                                          DEL PEAK 28(10P11.21) MUTATED
  ASIAN                                                                29
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                50
                                           clus
vv                                          DEL PEAK 28(10P11.21) WILD-TYPE
  ASIAN                                                                 100
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED     0  60
  DEL PEAK 28(10P11.21) WILD-TYPE   7 334
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED      0   60
  DEL PEAK 28(10P11.21) WILD-TYPE    7  334
                        clus
vv                       DEL PEAK 28(10P11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            60
                        clus
vv                       DEL PEAK 28(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             334
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 29(10Q21.1) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(10Q21.1) MUTATED    61  38
  DEL PEAK 29(10Q21.1) WILD-TYPE 293 183
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                            99                            476 
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                            38                            183 
$`DEL PEAK 29(10Q21.1) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A50L TCGA-IG-A5S3 
       14.30        13.94        33.27         0.85         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OE 
       14.50        68.02        23.18         3.16         0.30        24.00 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A8NK 
        4.70        21.01         1.38         3.16         4.90        13.55 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       27.12        83.24         0.10        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       22.39         0.10        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RC 
       12.00        12.03        13.18        53.95        15.78         3.42 
TCGA-V5-A7RE TCGA-VR-A8EX TCGA-Z6-A8JE TCGA-BR-6458 TCGA-BR-7723 TCGA-BR-7901 
        4.80        28.11         2.10        19.33        28.73         3.45 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A4CQ 
       14.43        11.44        16.31        17.52        20.22        22.26 
TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 
       13.15         0.07         0.10        12.20         7.99         4.01 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       12.03        18.97         4.01        19.13        18.84        18.54 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8578 TCGA-EQ-8122 
       10.26        15.98        12.79        18.21        21.14         7.99 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8249 TCGA-HU-8604 
       19.53         0.56         5.52         0.23        14.17        12.10 
TCGA-HU-A4GH TCGA-HU-A4GX TCGA-IN-8462 TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NR 
       11.77        10.19        18.81         1.41         6.74         6.51 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N6 TCGA-SW-A7EB 
       37.64         9.86        45.67         8.52         8.94         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
       48.79         5.46        13.02        18.48        35.24        22.19 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 
       17.85        36.69        18.74        21.04        11.24        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       32.94        29.98         0.79 

$`DEL PEAK 29(10Q21.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       25.78        31.27        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69         6.21        20.09 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
       20.78         2.63        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        60.39         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       42.77        25.41        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28        30.25         4.31         8.94         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS 
       19.99        47.93        18.35         3.32         7.17        58.59 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       29.00         7.13         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       25.12         0.36         7.40         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.76        12.59        15.52        11.54         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23         0.13        33.11         5.16         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV 
        9.30         2.89         1.45        12.69         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       20.38         5.29        15.35         9.27         4.44        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
       30.71        18.18        42.87        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       12.43         9.07        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         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       15.85         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.18         0.30         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-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       54.08        14.01        29.98        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       20.55        18.61        17.85        13.35        17.19        15.22 
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-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        14.66        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         0.62        16.24        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27        11.38         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       59.54         5.03        13.58        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.25         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 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       21.21         3.45         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08         6.44        12.59         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
       13.51         2.53         5.56        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       19.73        18.21        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       16.87        19.04         0.92        13.25        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       16.31         2.50        12.79         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        65.16        11.70        11.93        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       52.24         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
        5.72        64.18         2.66        42.54        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        17.13        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE 
                        13.150                         12.675 
[1] "0.1 - 83.2 (13.2)"  "0.0 - 122.3 (12.7)"
[1] "hr=" "1"  
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(10Q21.1) MUTATED         2        4        5        4        17
  DEL PEAK 29(10Q21.1) WILD-TYPE       9       15       43       28        60
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(10Q21.1) MUTATED          14         6         21          9
  DEL PEAK 29(10Q21.1) WILD-TYPE        70        23         76         63
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(10Q21.1) MUTATED            7        8         2
  DEL PEAK 29(10Q21.1) WILD-TYPE         41       43         2
D68V3, multiclass
            clus
vv           DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  STAGE I                               2                              9
  STAGE IA                              4                             15
  STAGE IB                              5                             43
  STAGE II                              4                             28
  STAGE IIA                            17                             60
  STAGE IIB                            14                             70
  STAGE III                             6                             23
  STAGE IIIA                           21                             76
  STAGE IIIB                            9                             63
  STAGE IIIC                            7                             41
  STAGE IV                              8                             43
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 29(10Q21.1) MUTATED       9  25  51  14
  DEL PEAK 29(10Q21.1) WILD-TYPE    44 101 229 110
D68V4, multiclass
       clus
vv      DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  T0+T1                            9                             44
  T2                              25                            101
  T3                              51                            229
  T4                              14                            110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 29(10Q21.1) MUTATED    33  30  19  17
  DEL PEAK 29(10Q21.1) WILD-TYPE 167 152  77  80
D68V5, multiclass
    clus
vv   DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  N0                           33                            167
  N1                           30                            152
  N2                           19                             77
  N3                           17                             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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q21.1) MUTATED    86   9
  DEL PEAK 29(10Q21.1) WILD-TYPE 427  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q21.1) MUTATED     86    9
  DEL PEAK 29(10Q21.1) WILD-TYPE  427   30
   clus
vv  DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  0                           86                            427
  1                            9                             30
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q21.1) MUTATED    31  75
  DEL PEAK 29(10Q21.1) WILD-TYPE 151 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q21.1) MUTATED     31   75
  DEL PEAK 29(10Q21.1) WILD-TYPE  151  352
        clus
vv       DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  FEMALE                           31                            151
  MALE                             75                            352
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 29(10Q21.1) MUTATED                                       5
  DEL PEAK 29(10Q21.1) WILD-TYPE                                    66
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(10Q21.1) MUTATED                                                       21
  DEL PEAK 29(10Q21.1) WILD-TYPE                                                    141
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(10Q21.1) MUTATED                                                                  15
  DEL PEAK 29(10Q21.1) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 29(10Q21.1) MUTATED                                                 16
  DEL PEAK 29(10Q21.1) WILD-TYPE                                               62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 29(10Q21.1) MUTATED                                                          4
  DEL PEAK 29(10Q21.1) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 29(10Q21.1) MUTATED                                                           2
  DEL PEAK 29(10Q21.1) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 29(10Q21.1) MUTATED                                          3
  DEL PEAK 29(10Q21.1) WILD-TYPE                                       10
D68V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 29(10Q21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 29(10Q21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              62
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q21.1) MUTATED     2 104
  DEL PEAK 29(10Q21.1) WILD-TYPE   4 499
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q21.1) MUTATED      2  104
  DEL PEAK 29(10Q21.1) WILD-TYPE    4  499
     clus
vv    DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  NO                             2                              4
  YES                          104                            499
[1] 2 2
[1] FALSE
D68V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(10Q21.1) MUTATED    53   2   3   4
  DEL PEAK 29(10Q21.1) WILD-TYPE 294  16  16  21
D68V11, multiclass
    clus
vv   DEL PEAK 29(10Q21.1) MUTATED DEL PEAK 29(10Q21.1) WILD-TYPE
  R0                           53                            294
  R1                            2                             16
  R2                            3                             16
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(10Q21.1) MUTATED      29                         5
  DEL PEAK 29(10Q21.1) WILD-TYPE   100                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(10Q21.1) MUTATED                                           0
  DEL PEAK 29(10Q21.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 29(10Q21.1) MUTATED      60
  DEL PEAK 29(10Q21.1) WILD-TYPE   325
D68V13, multiclass
                                           clus
vv                                          DEL PEAK 29(10Q21.1) MUTATED
  ASIAN                                                               29
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               60
                                           clus
vv                                          DEL PEAK 29(10Q21.1) WILD-TYPE
  ASIAN                                                                100
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q21.1) MUTATED     1  68
  DEL PEAK 29(10Q21.1) WILD-TYPE   6 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q21.1) MUTATED      1   68
  DEL PEAK 29(10Q21.1) WILD-TYPE    6  326
                        clus
vv                       DEL PEAK 29(10Q21.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 29(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            326
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 30(10Q22.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(10Q22.3) MUTATED    71  51
  DEL PEAK 30(10Q22.3) WILD-TYPE 283 170
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                           122                            453 
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                            51                            170 
$`DEL PEAK 30(10Q22.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-IG-A5S3 
       33.27        20.09         0.85         2.63         0.53        23.41 
TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       14.50        23.18         3.16         0.30         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OJ TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE 
        4.70        21.01         1.38         4.90         7.13        55.50 
TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y 
       13.55        27.12        83.24        12.66         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.49        22.39         0.10        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FU 
       12.33        25.25        12.00        12.23        12.03         5.16 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX 
       53.95         2.89         3.42         4.80        19.96        28.11 
TCGA-Z6-A8JE TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 
        2.10        28.01        28.73         3.45        11.44        16.31 
TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI 
       17.52         5.39        20.22        13.87        22.26        13.64 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A 
        3.25         0.30         0.07         0.10         3.42        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
        6.58        12.20         7.99         4.01        14.01        12.03 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 
       18.97        22.98        36.00         4.01        19.13        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT 
       10.26        15.22        15.98        12.79        21.14        14.27 
TCGA-D7-A4YX TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 
       15.16         7.99        19.53         5.52         0.23         5.92 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-IN-8462 TCGA-IN-A6RO 
       14.17        12.10        12.30        11.77        18.81         1.41 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR 
        6.74         6.51        37.64        45.67         8.52         6.08 
TCGA-R5-A805 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        9.24         8.94         5.79        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91N TCGA-VQ-A91U 
       18.48        22.19        17.85         1.87        18.74         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA68 
        9.50         9.73        64.18        21.04        11.24        40.08 
TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       32.94         0.79 

$`DEL PEAK 30(10Q22.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        58.55         7.63         8.94        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        6.21        20.78        20.12        18.64         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        12.82         9.96        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE 
       12.16       122.10        44.75        60.39        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       41.52        42.77        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28        30.25         8.94         3.68        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       19.99        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
       58.59        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       35.97        12.92        13.48        16.47        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.36         5.92        10.45        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35         0.10        13.25         0.10        12.76        12.59 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A9FO 
       15.52        11.54         4.47        10.52        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       33.11         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        7.04        29.59         6.35         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
       12.69         7.00        20.02        20.38         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        30.71        18.18        42.87        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       15.06        11.24         9.17        15.91        10.16         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        9.47         9.44         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        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 
       18.15        15.32        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       19.17        14.79         0.26        15.85         3.72        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
        9.86        15.68         8.22        10.68        12.56         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        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-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         9.34        11.31        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        1.02         8.05        54.08        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       21.99         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-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        69.04 
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-A4YY 
       18.21        14.66        20.91        16.44         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        2.96        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       13.58         0.56        18.08        26.47         1.51        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-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-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21        61.25         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V 
       11.70        11.93        61.22        20.81        22.68        36.16 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 
        6.58         5.72         2.66        42.54        22.09        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        29.98        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       21.11        12.43        10.62 

  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE 
                         12.38                          12.82 
[1] "0.1 - 83.2 (12.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(10Q22.3) MUTATED         2        4        6        6        20
  DEL PEAK 30(10Q22.3) WILD-TYPE       9       15       42       26        57
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(10Q22.3) MUTATED          20         9         22         12
  DEL PEAK 30(10Q22.3) WILD-TYPE        64        20         75         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(10Q22.3) MUTATED            8        9         2
  DEL PEAK 30(10Q22.3) WILD-TYPE         40       42         2
D69V3, multiclass
            clus
vv           DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  STAGE I                               2                              9
  STAGE IA                              4                             15
  STAGE IB                              6                             42
  STAGE II                              6                             26
  STAGE IIA                            20                             57
  STAGE IIB                            20                             64
  STAGE III                             9                             20
  STAGE IIIA                           22                             75
  STAGE IIIB                           12                             60
  STAGE IIIC                            8                             40
  STAGE IV                              9                             42
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 30(10Q22.3) MUTATED       9  32  64  15
  DEL PEAK 30(10Q22.3) WILD-TYPE    44  94 216 109
D69V4, multiclass
       clus
vv      DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  T0+T1                            9                             44
  T2                              32                             94
  T3                              64                            216
  T4                              15                            109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 30(10Q22.3) MUTATED    39  40  19  21
  DEL PEAK 30(10Q22.3) WILD-TYPE 161 142  77  76
D69V5, multiclass
    clus
vv   DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  N0                           39                            161
  N1                           40                            142
  N2                           19                             77
  N3                           21                             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"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(10Q22.3) MUTATED   109   9
  DEL PEAK 30(10Q22.3) WILD-TYPE 404  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(10Q22.3) MUTATED    109    9
  DEL PEAK 30(10Q22.3) WILD-TYPE  404   30
   clus
vv  DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  0                          109                            404
  1                            9                             30
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(10Q22.3) MUTATED    33  95
  DEL PEAK 30(10Q22.3) WILD-TYPE 149 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(10Q22.3) MUTATED     33   95
  DEL PEAK 30(10Q22.3) WILD-TYPE  149  332
        clus
vv       DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  FEMALE                           33                            149
  MALE                             95                            332
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 30(10Q22.3) MUTATED                                       5
  DEL PEAK 30(10Q22.3) WILD-TYPE                                    66
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(10Q22.3) MUTATED                                                       25
  DEL PEAK 30(10Q22.3) WILD-TYPE                                                    137
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(10Q22.3) MUTATED                                                                  19
  DEL PEAK 30(10Q22.3) WILD-TYPE                                                                62
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 30(10Q22.3) MUTATED                                                 19
  DEL PEAK 30(10Q22.3) WILD-TYPE                                               59
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 30(10Q22.3) MUTATED                                                          3
  DEL PEAK 30(10Q22.3) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 30(10Q22.3) MUTATED                                                           2
  DEL PEAK 30(10Q22.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 30(10Q22.3) MUTATED                                          4
  DEL PEAK 30(10Q22.3) WILD-TYPE                                        9
D69V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 30(10Q22.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 30(10Q22.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(10Q22.3) MUTATED     1 127
  DEL PEAK 30(10Q22.3) WILD-TYPE   5 476
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(10Q22.3) MUTATED      1  127
  DEL PEAK 30(10Q22.3) WILD-TYPE    5  476
     clus
vv    DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  NO                             1                              5
  YES                          127                            476
[1] 2 2
[1] FALSE
D69V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(10Q22.3) MUTATED    57   2   4   4
  DEL PEAK 30(10Q22.3) WILD-TYPE 290  16  15  21
D69V11, multiclass
    clus
vv   DEL PEAK 30(10Q22.3) MUTATED DEL PEAK 30(10Q22.3) WILD-TYPE
  R0                           57                            290
  R1                            2                             16
  R2                            4                             15
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(10Q22.3) MUTATED      34                         6
  DEL PEAK 30(10Q22.3) WILD-TYPE    95                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(10Q22.3) MUTATED                                           0
  DEL PEAK 30(10Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 30(10Q22.3) MUTATED      69
  DEL PEAK 30(10Q22.3) WILD-TYPE   316
D69V13, multiclass
                                           clus
vv                                          DEL PEAK 30(10Q22.3) MUTATED
  ASIAN                                                               34
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               69
                                           clus
vv                                          DEL PEAK 30(10Q22.3) WILD-TYPE
  ASIAN                                                                 95
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(10Q22.3) MUTATED     1  80
  DEL PEAK 30(10Q22.3) WILD-TYPE   6 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(10Q22.3) MUTATED      1   80
  DEL PEAK 30(10Q22.3) WILD-TYPE    6  314
                        clus
vv                       DEL PEAK 30(10Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK 30(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            314
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 31(10Q23.31) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 31(10Q23.31) MUTATED    96  73
  DEL PEAK 31(10Q23.31) WILD-TYPE 258 148
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                            169                             406 
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                             73                             148 
$`DEL PEAK 31(10Q23.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        14.30         5.92        13.94        16.24         4.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L 
       33.27        20.09         0.85         2.63        18.64         0.53 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H 
       23.41        14.50        44.75        23.18         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE 
        3.32         3.16        58.59         4.90         7.13        55.50 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       13.48        13.55        27.12        83.24        10.45        12.66 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 
       13.41         0.10        12.46        12.59        12.49        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
        0.10        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6Y0 
       12.00        12.03         5.16         7.59         5.06        53.95 
TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX TCGA-Z6-A8JE 
        2.89         3.42         4.80        19.96        28.11         2.10 
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7716 
       11.70         6.61        18.35        13.87        35.24        28.01 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 
       28.73         3.45        17.49        11.44        16.31         2.20 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       17.52         4.31        14.04         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
       20.22         9.86        22.26        13.64         3.25         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A 
        0.07         0.07         0.07         0.10         3.42        12.43 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       12.20        27.02         7.99         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 
       47.05        12.03        21.99        18.97        36.00        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
        4.01        69.04        12.36        19.13        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 
       15.22        15.98        12.79        21.14        14.27         2.96 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99         3.48        19.53        13.58         0.56         5.52 
TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GT 
        0.23         5.92        14.17        12.10        11.77         6.51 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO 
        6.25        12.30        27.42        18.81        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A93H TCGA-R5-A7O7 
        6.44         6.74         6.51         1.81        37.64        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.52         6.08         9.24         8.94         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       48.79         5.46        13.02        18.48        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X 
        1.87        13.35        36.69        18.74         1.71         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73         9.04         5.72        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I 
       11.24        18.41        40.08        32.94        26.04        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 31(10Q23.31) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        58.55         7.63         8.94        32.45         7.69 
TCGA-IC-A6RF TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
        6.21        20.78        20.12         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        0.79        12.82         9.96        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       30.25         3.68        19.99        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V 
        1.38        29.00         7.43         6.94         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
       25.12         0.36         7.40         3.95         3.02         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        13.41        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
        5.92        12.43        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
        0.10        12.76        12.59        15.52        11.54         4.47 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23        13.18         0.13        33.11         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       14.70         7.04        29.59         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         4.44        18.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        3.42         2.66        19.73        26.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         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-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42        18.15        15.32        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        14.43         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       20.55         8.05         0.56        12.95         2.66        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        0.95        26.33         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.26        15.85         3.72         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-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         9.34        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 
        6.58         0.10        12.62        20.02         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        1.02         8.05        54.08        19.07         0.00         9.01 
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-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       79.07        65.10        21.07         7.99        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85        13.35        17.19 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76        15.65         8.38         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       11.38        14.07        22.29        17.06        59.54         5.03 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        23.84         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39         5.36         5.19        13.08        12.59 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       20.15         3.72        19.73         9.86        18.21        61.25 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       35.61        16.87        19.04        13.25        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       46.26        16.31         2.50        12.79         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       65.16        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       36.16         7.36        52.24         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        6.58         2.66        22.09        28.41        29.98        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        21.11        12.43        10.62 

  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                          83.24                          122.30 
  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE 
                          12.43                           12.82 
[1] "0.1 - 83.2 (12.4)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D70V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(10Q23.31) MUTATED         4        5       13        8        24
  DEL PEAK 31(10Q23.31) WILD-TYPE       7       14       35       24        53
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(10Q23.31) MUTATED          25        10         29         17
  DEL PEAK 31(10Q23.31) WILD-TYPE        59        19         68         55
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(10Q23.31) MUTATED           12       14         2
  DEL PEAK 31(10Q23.31) WILD-TYPE         36       37         2
D70V3, multiclass
            clus
vv           DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  STAGE I                                4                               7
  STAGE IA                               5                              14
  STAGE IB                              13                              35
  STAGE II                               8                              24
  STAGE IIA                             24                              53
  STAGE IIB                             25                              59
  STAGE III                             10                              19
  STAGE IIIA                            29                              68
  STAGE IIIB                            17                              55
  STAGE IIIC                            12                              36
  STAGE IV                              14                              37
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 31(10Q23.31) MUTATED      13  45  83  23
  DEL PEAK 31(10Q23.31) WILD-TYPE    40  81 197 101
D70V4, multiclass
       clus
vv      DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  T0+T1                            13                              40
  T2                               45                              81
  T3                               83                             197
  T4                               23                             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 31(10Q23.31) MUTATED    56  52  26  30
  DEL PEAK 31(10Q23.31) WILD-TYPE 144 130  70  67
D70V5, multiclass
    clus
vv   DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  N0                            56                             144
  N1                            52                             130
  N2                            26                              70
  N3                            30                              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                                 cls
clus                                0   1
  DEL PEAK 31(10Q23.31) MUTATED   149  10
  DEL PEAK 31(10Q23.31) WILD-TYPE 364  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(10Q23.31) MUTATED    149   10
  DEL PEAK 31(10Q23.31) WILD-TYPE  364   29
   clus
vv  DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  0                           149                             364
  1                            10                              29
[1] 2 2
[1] FALSE
D70V7, binary
                                 cls
clus                                0   1
  DEL PEAK 31(10Q23.31) MUTATED    50 125
  DEL PEAK 31(10Q23.31) WILD-TYPE 132 302
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(10Q23.31) MUTATED     50  125
  DEL PEAK 31(10Q23.31) WILD-TYPE  132  302
        clus
vv       DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  FEMALE                            50                             132
  MALE                             125                             302
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 31(10Q23.31) MUTATED                                       7
  DEL PEAK 31(10Q23.31) WILD-TYPE                                    64
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(10Q23.31) MUTATED                                                       39
  DEL PEAK 31(10Q23.31) WILD-TYPE                                                    123
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(10Q23.31) MUTATED                                                                  31
  DEL PEAK 31(10Q23.31) WILD-TYPE                                                                50
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 31(10Q23.31) MUTATED                                                 25
  DEL PEAK 31(10Q23.31) WILD-TYPE                                               53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 31(10Q23.31) MUTATED                                                          5
  DEL PEAK 31(10Q23.31) WILD-TYPE                                                       16
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 31(10Q23.31) MUTATED                                                           3
  DEL PEAK 31(10Q23.31) WILD-TYPE                                                         5
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 31(10Q23.31) MUTATED                                          4
  DEL PEAK 31(10Q23.31) WILD-TYPE                                        9
D70V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 31(10Q23.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      4
                                                                   clus
vv                                                                  DEL PEAK 31(10Q23.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        123
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                                 cls
clus                                0   1
  DEL PEAK 31(10Q23.31) MUTATED     1 174
  DEL PEAK 31(10Q23.31) WILD-TYPE   5 429
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(10Q23.31) MUTATED      1  174
  DEL PEAK 31(10Q23.31) WILD-TYPE    5  429
     clus
vv    DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  NO                              1                               5
  YES                           174                             429
[1] 2 2
[1] FALSE
D70V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 31(10Q23.31) MUTATED    90   3   5   6
  DEL PEAK 31(10Q23.31) WILD-TYPE 257  15  14  19
D70V11, multiclass
    clus
vv   DEL PEAK 31(10Q23.31) MUTATED DEL PEAK 31(10Q23.31) WILD-TYPE
  R0                            90                             257
  R1                             3                              15
  R2                             5                              14
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(10Q23.31) MUTATED      42                         7
  DEL PEAK 31(10Q23.31) WILD-TYPE    87                         6
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(10Q23.31) MUTATED                                           0
  DEL PEAK 31(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 31(10Q23.31) MUTATED     100
  DEL PEAK 31(10Q23.31) WILD-TYPE   285
D70V13, multiclass
                                           clus
vv                                          DEL PEAK 31(10Q23.31) MUTATED
  ASIAN                                                                42
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               100
                                           clus
vv                                          DEL PEAK 31(10Q23.31) WILD-TYPE
  ASIAN                                                                  87
  BLACK OR AFRICAN AMERICAN                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                                 cls
clus                                0   1
  DEL PEAK 31(10Q23.31) MUTATED     1 107
  DEL PEAK 31(10Q23.31) WILD-TYPE   6 287
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(10Q23.31) MUTATED      1  107
  DEL PEAK 31(10Q23.31) WILD-TYPE    6  287
                        clus
vv                       DEL PEAK 31(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           107
                        clus
vv                       DEL PEAK 31(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             287
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 32(11P15.5) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(11P15.5) MUTATED   102  62
  DEL PEAK 32(11P15.5) WILD-TYPE 252 159
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                           164                            411 
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                            62                            159 
$`DEL PEAK 32(11P15.5) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        14.30         5.92         4.21        32.45         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43C 
        0.85         2.63         0.53        25.41        25.22         3.16 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
        0.30         4.31         8.94         4.70        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y 
        7.17         1.38         3.16         6.94         2.60         0.36 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.95         3.02        55.50        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.22        13.41        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       12.43        13.41         0.10        13.15        15.35         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.49        12.76         0.10        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO 
        4.47        12.33        25.25        12.00        12.03         0.13 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       29.59        53.95        15.78         1.45        12.69        20.02 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER 
        3.42         4.80         9.27         4.44        19.96        12.43 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE 
        8.12        28.11        18.18        11.24        15.91         2.10 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7703 
        6.61         6.97        18.35         9.57        26.10        24.76 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8297 
       35.24        15.42        28.01        28.73         9.60         7.40 
TCGA-BR-8369 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CD-5800 
       14.04         1.48         0.72         0.53         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4304 
        0.30         0.07         0.07         0.07        12.43        27.02 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5717 
       29.98        47.05        19.07        21.99        18.97         6.97 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02         4.01        69.04        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       20.55        18.84        18.54        10.26        15.22        15.98 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C 
       21.14        14.27         7.40         0.62        72.23        11.38 
TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GD TCGA-HU-A4H0 
       13.58        26.47         5.92        12.59        22.75         2.10 
TCGA-HU-A4H5 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       12.30        18.81         3.39        18.38         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.44         6.74         2.53        37.64        45.67        18.21 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67        37.91         8.94        35.61        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        18.48        34.45        32.48         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91E 
       22.19        17.85        13.35        27.35        14.33        11.93 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94U 
        9.73        52.24         4.54        21.04        42.54        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 
       18.41        40.08 

$`DEL PEAK 32(11P15.5) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        58.55         7.63        13.94         8.94        16.24 
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
        6.21        33.27        20.09        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         9.30        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       44.75        60.39        68.02         3.68        41.52        42.77 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        23.18        31.56        24.03         6.28        30.25 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       24.00         3.68        19.99        21.01        47.93        18.35 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88T 
       58.59         4.90        29.00         7.13         7.43         8.71 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NM 
       25.12         7.40         2.66        35.97        12.92         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        5.49        21.37         8.71        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       46.09         0.10        13.25        12.46        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-M9-A5M8 
       15.52        11.54        10.52        12.23        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        5.16         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
        7.04         6.35         9.30         2.89         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        5.29        15.35        18.81        22.82         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR 
       30.71        42.87        46.19        15.06         9.17        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       11.01         9.47         9.44         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7717 
       31.20        32.94        12.82         9.21        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49        14.43        11.44         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        12.95         2.66        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       12.56        13.87         7.53         6.08        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51        12.89         8.98        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 
       13.64        11.57         5.13         2.83        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         3.42         9.34        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        4.01        14.01        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98        30.97        36.00         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-D7-6518 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.36        19.13        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        17.19        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.65         8.38         4.34         7.13         7.99        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        59.54         5.03         0.56         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51        14.27        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        23.84         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS 
       27.42        21.21         3.45         5.36         1.41        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
        6.51         5.56         1.81         7.82        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       60.56        20.15         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.13       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E2 
       57.44        16.87        19.04         5.79         0.92        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       21.73        27.88        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        26.24        64.57        65.16        36.69        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         9.50         9.04         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        64.18         2.66        11.24        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       29.98        17.13        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE 
                         12.66                          12.79 
[1] "0.1 - 72.2 (12.7)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(11P15.5) MUTATED         4        5       11       12        21
  DEL PEAK 32(11P15.5) WILD-TYPE       7       14       37       20        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(11P15.5) MUTATED          16        14         31         14
  DEL PEAK 32(11P15.5) WILD-TYPE        68        15         66         58
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(11P15.5) MUTATED           13       12         2
  DEL PEAK 32(11P15.5) WILD-TYPE         35       39         2
D71V3, multiclass
            clus
vv           DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              5                             14
  STAGE IB                             11                             37
  STAGE II                             12                             20
  STAGE IIA                            21                             56
  STAGE IIB                            16                             68
  STAGE III                            14                             15
  STAGE IIIA                           31                             66
  STAGE IIIB                           14                             58
  STAGE IIIC                           13                             35
  STAGE IV                             12                             39
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 32(11P15.5) MUTATED      15  42  81  21
  DEL PEAK 32(11P15.5) WILD-TYPE    38  84 199 103
D71V4, multiclass
       clus
vv      DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  T0+T1                           15                             38
  T2                              42                             84
  T3                              81                            199
  T4                              21                            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 32(11P15.5) MUTATED    54  57  24  25
  DEL PEAK 32(11P15.5) WILD-TYPE 146 125  72  72
D71V5, multiclass
    clus
vv   DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  N0                           54                            146
  N1                           57                            125
  N2                           24                             72
  N3                           25                             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"
D71V6, binary
                                cls
clus                               0   1
  DEL PEAK 32(11P15.5) MUTATED   137  11
  DEL PEAK 32(11P15.5) WILD-TYPE 376  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(11P15.5) MUTATED    137   11
  DEL PEAK 32(11P15.5) WILD-TYPE  376   28
   clus
vv  DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  0                          137                            376
  1                           11                             28
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(11P15.5) MUTATED    37 133
  DEL PEAK 32(11P15.5) WILD-TYPE 145 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(11P15.5) MUTATED     37  133
  DEL PEAK 32(11P15.5) WILD-TYPE  145  294
        clus
vv       DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  FEMALE                           37                            145
  MALE                            133                            294
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 32(11P15.5) MUTATED                                       9
  DEL PEAK 32(11P15.5) WILD-TYPE                                    62
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(11P15.5) MUTATED                                                       31
  DEL PEAK 32(11P15.5) WILD-TYPE                                                    131
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(11P15.5) MUTATED                                                                  21
  DEL PEAK 32(11P15.5) WILD-TYPE                                                                60
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 32(11P15.5) MUTATED                                                 23
  DEL PEAK 32(11P15.5) WILD-TYPE                                               55
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 32(11P15.5) MUTATED                                                          5
  DEL PEAK 32(11P15.5) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 32(11P15.5) MUTATED                                                           5
  DEL PEAK 32(11P15.5) WILD-TYPE                                                         3
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 32(11P15.5) MUTATED                                          3
  DEL PEAK 32(11P15.5) WILD-TYPE                                       10
D71V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 32(11P15.5) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 32(11P15.5) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(11P15.5) MUTATED     1 169
  DEL PEAK 32(11P15.5) WILD-TYPE   5 434
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(11P15.5) MUTATED      1  169
  DEL PEAK 32(11P15.5) WILD-TYPE    5  434
     clus
vv    DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  NO                             1                              5
  YES                          169                            434
[1] 2 2
[1] FALSE
D71V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(11P15.5) MUTATED    74   3   7   8
  DEL PEAK 32(11P15.5) WILD-TYPE 273  15  12  17
D71V11, multiclass
    clus
vv   DEL PEAK 32(11P15.5) MUTATED DEL PEAK 32(11P15.5) WILD-TYPE
  R0                           74                            273
  R1                            3                             15
  R2                            7                             12
  RX                            8                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(11P15.5) MUTATED      41                         5
  DEL PEAK 32(11P15.5) WILD-TYPE    88                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(11P15.5) MUTATED                                           0
  DEL PEAK 32(11P15.5) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 32(11P15.5) MUTATED     103
  DEL PEAK 32(11P15.5) WILD-TYPE   282
D71V13, multiclass
                                           clus
vv                                          DEL PEAK 32(11P15.5) MUTATED
  ASIAN                                                               41
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              103
                                           clus
vv                                          DEL PEAK 32(11P15.5) WILD-TYPE
  ASIAN                                                                 88
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                                cls
clus                               0   1
  DEL PEAK 32(11P15.5) MUTATED     2  98
  DEL PEAK 32(11P15.5) WILD-TYPE   5 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(11P15.5) MUTATED      2   98
  DEL PEAK 32(11P15.5) WILD-TYPE    5  296
                        clus
vv                       DEL PEAK 32(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           98
                        clus
vv                       DEL PEAK 32(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 33(11Q25) MUTATION ANALYSIS
D72V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 33(11Q25) MUTATED    96  67
  DEL PEAK 33(11Q25) WILD-TYPE 258 154
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                         163                          412 
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                          67                          154 
$`DEL PEAK 33(11Q25) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
       14.30         7.63         5.92        20.12        18.64         3.88 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FH 
       17.03        23.41         9.96        14.50        12.16        42.77 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        3.16         0.30         3.68        47.93         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
        3.16        29.00         6.94         2.60         3.95         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NT 
       55.50        12.92        16.47        13.55        13.22        27.12 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10        13.25        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       22.39         0.10        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW 
       25.25        12.00        12.23         0.13         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        8.02         7.59         5.06         2.89         1.45        12.69 
TCGA-S8-A6BV TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       20.02         3.42        18.81        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       28.11        18.18        11.24         9.17        15.91         2.10 
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
        6.97        18.35         6.18         9.57        17.29        13.68 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 
       26.10        12.16        15.42        17.49        11.44         9.60 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A4CQ 
        2.66         7.40        17.52        20.22         8.22        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        1.48         0.72        13.51         1.15        13.64         3.25 
TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 
       13.15         0.07         0.10        12.43         8.05        29.98 
TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 
       12.03        36.00        12.03        12.66        11.93        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A6EV 
       17.19        10.26        15.22        15.98        18.21        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7916 
       11.31         9.76         7.40         0.62        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 
       17.06        13.58         0.56        26.47         5.92        14.17 
TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
        0.76         3.25        22.75        11.77         6.25         2.10 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IP-7968 
       23.84         9.67         1.41         6.44         5.56         2.53 
TCGA-R5-A7O7 TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       45.67         9.24       122.30        37.91       115.69         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS 
       48.79        13.25         7.73         2.70        17.85        13.35 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       36.69        20.81        22.68         9.50        52.24         9.04 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       21.04        42.54        11.24        17.13        54.12        26.04 
TCGA-VQ-AA6K 
       12.43 

$`DEL PEAK 33(11Q25) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       25.78        31.27        58.55        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        4.21        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
        0.85        20.78         2.63         9.30         0.53         0.79 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C 
       68.02         3.68        41.52        25.41        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J 
       31.56        25.22        24.03         6.28        30.25         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        8.94        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
       18.35         1.38        58.59         4.90         7.13         7.43 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71        25.12         0.36         7.40         2.66        35.97 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       83.24        46.09        13.41        13.15        15.35         0.10 
TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY 
       12.46        12.59        11.54         4.47        10.52        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       13.18        33.11        14.70         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30        15.78         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
        4.80        15.35         9.27         4.44        19.96        22.82 
TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-X8-AAAR 
        1.55        30.71        42.87        46.19        15.06        10.16 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.66        19.73        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
       30.90         6.61        34.68        15.95        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       18.71        14.43         0.69        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.56        12.95        16.31         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        19.36         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
       54.08         4.01        14.01        47.05        19.07        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-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-D7-6518 TCGA-D7-6519 
       69.04        21.07         7.99        12.36        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.61        17.85        13.35        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 
       15.16        13.78        14.76        13.71        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
       15.65         8.38         4.34         7.13         7.99        16.24 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 
       14.47        72.23        21.27        11.38         3.48        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       59.54         5.03         5.52         0.23        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       14.27        12.59        11.41        12.10        10.62        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        12.30        11.84        24.20        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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        19.36        12.30         8.88         8.81        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-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
        5.19        13.08         6.74        12.59         6.51         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        7.82        13.51         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60        11.05         8.61         5.13        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         5.79         0.92         5.46        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        26.24        27.35 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        65.16        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       18.74         1.71        36.16         7.36         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        64.18         2.66 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        10.62         0.79 

  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                       122.3                        122.1 
  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE 
                       12.33                        13.05 
[1] "0.1 - 122.3 (12.3)" "0.0 - 122.1 (13.1)"
[1] "hr=" "1.3"
D72V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(11Q25) MUTATED         1        8        5       10        27
  DEL PEAK 33(11Q25) WILD-TYPE      10       11       43       22        50
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(11Q25) MUTATED          20        13         24         21
  DEL PEAK 33(11Q25) WILD-TYPE        64        16         73         51
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(11Q25) MUTATED           14       12         1
  DEL PEAK 33(11Q25) WILD-TYPE         34       39         3
D72V3, multiclass
            clus
vv           DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  STAGE I                             1                           10
  STAGE IA                            8                           11
  STAGE IB                            5                           43
  STAGE II                           10                           22
  STAGE IIA                          27                           50
  STAGE IIB                          20                           64
  STAGE III                          13                           16
  STAGE IIIA                         24                           73
  STAGE IIIB                         21                           51
  STAGE IIIC                         14                           34
  STAGE IV                           12                           39
  STAGE IVA                           1                            3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  DEL PEAK 33(11Q25) MUTATED      15  36  84  23
  DEL PEAK 33(11Q25) WILD-TYPE    38  90 196 101
D72V4, multiclass
       clus
vv      DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  T0+T1                         15                           38
  T2                            36                           90
  T3                            84                          196
  T4                            23                          101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 33(11Q25) MUTATED    48  51  34  24
  DEL PEAK 33(11Q25) WILD-TYPE 152 131  62  73
D72V5, multiclass
    clus
vv   DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  N0                         48                          152
  N1                         51                          131
  N2                         34                           62
  N3                         24                           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"
D72V6, binary
                              cls
clus                             0   1
  DEL PEAK 33(11Q25) MUTATED   136   9
  DEL PEAK 33(11Q25) WILD-TYPE 377  30
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(11Q25) MUTATED    136    9
  DEL PEAK 33(11Q25) WILD-TYPE  377   30
   clus
vv  DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  0                        136                          377
  1                          9                           30
[1] 2 2
[1] FALSE
D72V7, binary
                              cls
clus                             0   1
  DEL PEAK 33(11Q25) MUTATED    37 131
  DEL PEAK 33(11Q25) WILD-TYPE 145 296
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(11Q25) MUTATED     37  131
  DEL PEAK 33(11Q25) WILD-TYPE  145  296
        clus
vv       DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  FEMALE                         37                          145
  MALE                          131                          296
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 33(11Q25) MUTATED                                      10
  DEL PEAK 33(11Q25) WILD-TYPE                                    61
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(11Q25) MUTATED                                                       33
  DEL PEAK 33(11Q25) WILD-TYPE                                                    129
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(11Q25) MUTATED                                                                  22
  DEL PEAK 33(11Q25) WILD-TYPE                                                                59
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 33(11Q25) MUTATED                                                 21
  DEL PEAK 33(11Q25) WILD-TYPE                                               57
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 33(11Q25) MUTATED                                                          6
  DEL PEAK 33(11Q25) WILD-TYPE                                                       15
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 33(11Q25) MUTATED                                                           2
  DEL PEAK 33(11Q25) WILD-TYPE                                                         6
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 33(11Q25) MUTATED                                          2
  DEL PEAK 33(11Q25) WILD-TYPE                                       11
D72V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 33(11Q25) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   2
                                                                   clus
vv                                                                  DEL PEAK 33(11Q25) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     129
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                              cls
clus                             0   1
  DEL PEAK 33(11Q25) MUTATED     1 167
  DEL PEAK 33(11Q25) WILD-TYPE   5 436
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(11Q25) MUTATED      1  167
  DEL PEAK 33(11Q25) WILD-TYPE    5  436
     clus
vv    DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  NO                           1                            5
  YES                        167                          436
[1] 2 2
[1] FALSE
D72V10, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 33(11Q25) MUTATED    75   7   3   6
  DEL PEAK 33(11Q25) WILD-TYPE 272  11  16  19
D72V11, multiclass
    clus
vv   DEL PEAK 33(11Q25) MUTATED DEL PEAK 33(11Q25) WILD-TYPE
  R0                         75                          272
  R1                          7                           11
  R2                          3                           16
  RX                          6                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(11Q25) MUTATED      41                         3
  DEL PEAK 33(11Q25) WILD-TYPE    88                        10
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 33(11Q25) MUTATED                                           0   106
  DEL PEAK 33(11Q25) WILD-TYPE                                         1   279
D72V13, multiclass
                                           clus
vv                                          DEL PEAK 33(11Q25) MUTATED
  ASIAN                                                             41
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                            106
                                           clus
vv                                          DEL PEAK 33(11Q25) WILD-TYPE
  ASIAN                                                               88
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                              cls
clus                             0   1
  DEL PEAK 33(11Q25) MUTATED     2 108
  DEL PEAK 33(11Q25) WILD-TYPE   5 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(11Q25) MUTATED      2  108
  DEL PEAK 33(11Q25) WILD-TYPE    5  286
                        clus
vv                       DEL PEAK 33(11Q25) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        108
                        clus
vv                       DEL PEAK 33(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          286
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 34(12P13.1) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(12P13.1) MUTATED    59  46
  DEL PEAK 34(12P13.1) WILD-TYPE 295 175
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                           105                            470 
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                            46                            175 
$`DEL PEAK 34(12P13.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 
       25.78        13.94        32.45        33.27         3.88         0.79 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M 
       42.77        25.41        31.56        25.22        30.25         8.94 
TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NN 
        7.13         6.94         3.95         3.02        12.92         5.49 
TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A7HW TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FW 
       52.57        12.66        12.00        12.03        33.11         7.82 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-S8-A6BV TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        5.06        29.59        20.02        10.16         2.10        19.73 
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7704 
        6.61         6.18        17.29        19.33        12.16        35.24 
TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8369 
       15.42         3.45        11.44         2.66        13.08        14.04 
TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5800 TCGA-CD-8524 
        5.39        11.54         9.86        22.26        13.15         0.07 
TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
        0.07         0.13         3.42        11.31        12.43        12.20 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 
        3.02         7.99        14.01        30.97        15.02        69.04 
TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A74A 
       20.55        15.22        12.79        12.33        14.27         7.40 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-HU-8245 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.62         7.99        72.23        12.59        23.84        12.30 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A7NU TCGA-IP-7968 TCGA-R5-A7O7 
        3.39        18.38         5.19         1.81         2.53        45.67 
TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PJ 
       37.91        35.61         5.46        13.02        32.48         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
        1.87        14.33        18.74         1.71        36.16         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       52.24         9.04         2.01         5.72        64.18        21.04 
TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       17.13        16.14         0.79 

$`DEL PEAK 34(12P13.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69         6.21        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03        23.41        12.82         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
       14.50        12.16       122.10        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        23.18        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        3.16         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU 
       19.99        21.01        47.93        18.35         3.16        29.00 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
       55.50         2.66        35.97        13.48        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
       13.22         7.76        21.37         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       83.24        46.09        10.36         5.92        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        10.52        12.23        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         5.16         8.02         7.59        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        6.35        53.95         9.30        15.78         2.89         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.69         7.00        20.38         5.29         3.42         4.80 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         4.44        18.81        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        42.87        46.19        15.06        11.24         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       15.91         3.42         2.66        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.87        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       28.01        18.15        15.32        28.73        12.43         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         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-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         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         8.22        10.68        12.56        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-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         9.34 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
       11.61         6.58         0.10        12.62        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-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        22.98         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 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-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.13        16.24        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         5.52         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-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-A4H6 TCGA-HU-A4H8 
        0.26         2.10        12.95        19.36         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-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.08         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        5.56         7.82        13.51         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       37.64         3.72        19.73         9.86        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.25        18.48        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       34.45        27.88         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PO 
       16.31        22.19         2.50        12.79        17.85         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
       23.41        15.65        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       65.16        36.69        11.70        11.93        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       22.68         7.36         9.73        55.43         4.54         6.58 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
        2.66        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       28.41        32.94        29.98        54.12        26.04        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        10.62 

  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE 
                         12.33                          12.82 
[1] "0.1 - 72.2 (12.3)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.2"
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(12P13.1) MUTATED         4        2       12        5        12
  DEL PEAK 34(12P13.1) WILD-TYPE       7       17       36       27        65
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(12P13.1) MUTATED          12         3         22         11
  DEL PEAK 34(12P13.1) WILD-TYPE        72        26         75         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(12P13.1) MUTATED            7       13         0
  DEL PEAK 34(12P13.1) WILD-TYPE         41       38         4
D73V3, multiclass
            clus
vv           DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              2                             17
  STAGE IB                             12                             36
  STAGE II                              5                             27
  STAGE IIA                            12                             65
  STAGE IIB                            12                             72
  STAGE III                             3                             26
  STAGE IIIA                           22                             75
  STAGE IIIB                           11                             61
  STAGE IIIC                            7                             41
  STAGE IV                             13                             38
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 34(12P13.1) MUTATED       8  29  54  15
  DEL PEAK 34(12P13.1) WILD-TYPE    45  97 226 109
D73V4, multiclass
       clus
vv      DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  T0+T1                            8                             45
  T2                              29                             97
  T3                              54                            226
  T4                              15                            109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 34(12P13.1) MUTATED    35  34  18  19
  DEL PEAK 34(12P13.1) WILD-TYPE 165 148  78  78
D73V5, multiclass
    clus
vv   DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  N0                           35                            165
  N1                           34                            148
  N2                           18                             78
  N3                           19                             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"
D73V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(12P13.1) MUTATED    89   8
  DEL PEAK 34(12P13.1) WILD-TYPE 424  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12P13.1) MUTATED     89    8
  DEL PEAK 34(12P13.1) WILD-TYPE  424   31
   clus
vv  DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  0                           89                            424
  1                            8                             31
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(12P13.1) MUTATED    34  76
  DEL PEAK 34(12P13.1) WILD-TYPE 148 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12P13.1) MUTATED     34   76
  DEL PEAK 34(12P13.1) WILD-TYPE  148  351
        clus
vv       DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  FEMALE                           34                            148
  MALE                             76                            351
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 34(12P13.1) MUTATED                                       3
  DEL PEAK 34(12P13.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(12P13.1) MUTATED                                                       30
  DEL PEAK 34(12P13.1) WILD-TYPE                                                    132
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(12P13.1) MUTATED                                                                  15
  DEL PEAK 34(12P13.1) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 34(12P13.1) MUTATED                                                 20
  DEL PEAK 34(12P13.1) WILD-TYPE                                               58
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 34(12P13.1) MUTATED                                                          0
  DEL PEAK 34(12P13.1) WILD-TYPE                                                       21
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 34(12P13.1) MUTATED                                                           4
  DEL PEAK 34(12P13.1) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 34(12P13.1) MUTATED                                          2
  DEL PEAK 34(12P13.1) WILD-TYPE                                       11
D73V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 34(12P13.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     2
                                                                   clus
vv                                                                  DEL PEAK 34(12P13.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(12P13.1) MUTATED     3 107
  DEL PEAK 34(12P13.1) WILD-TYPE   3 496
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12P13.1) MUTATED      3  107
  DEL PEAK 34(12P13.1) WILD-TYPE    3  496
     clus
vv    DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  NO                             3                              3
  YES                          107                            496
[1] 2 2
[1] FALSE
D73V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(12P13.1) MUTATED    57   2   4   5
  DEL PEAK 34(12P13.1) WILD-TYPE 290  16  15  20
D73V11, multiclass
    clus
vv   DEL PEAK 34(12P13.1) MUTATED DEL PEAK 34(12P13.1) WILD-TYPE
  R0                           57                            290
  R1                            2                             16
  R2                            4                             15
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(12P13.1) MUTATED      17                         3
  DEL PEAK 34(12P13.1) WILD-TYPE   112                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(12P13.1) MUTATED                                           0
  DEL PEAK 34(12P13.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 34(12P13.1) MUTATED      71
  DEL PEAK 34(12P13.1) WILD-TYPE   314
D73V13, multiclass
                                           clus
vv                                          DEL PEAK 34(12P13.1) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               71
                                           clus
vv                                          DEL PEAK 34(12P13.1) WILD-TYPE
  ASIAN                                                                112
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                                cls
clus                               0   1
  DEL PEAK 34(12P13.1) MUTATED     1  60
  DEL PEAK 34(12P13.1) WILD-TYPE   6 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12P13.1) MUTATED      1   60
  DEL PEAK 34(12P13.1) WILD-TYPE    6  334
                        clus
vv                       DEL PEAK 34(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 34(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 35(12Q23.1) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(12Q23.1) MUTATED    60  42
  DEL PEAK 35(12Q23.1) WILD-TYPE 294 179
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                           102                            473 
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                            42                            179 
$`DEL PEAK 35(12Q23.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78        31.27        14.30        13.94        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD 
        2.63        18.64         0.79        23.41        14.50        68.02 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH 
       42.77        25.41        25.22        30.25         8.94        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V 
       21.01         3.32         7.17        58.59         7.13         2.60 
TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NS TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-Q9-A6FW 
       13.41        12.66        13.41        12.59        12.33         7.82 
TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX 
        5.06         2.89        20.02        20.38         3.42         4.44 
TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-BR-4183 
        1.55        42.87        11.24        10.16         2.66         6.61 
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 
       17.29        35.24        15.42         3.45        11.44        12.95 
TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ 
        7.40         5.39         9.21         9.86         8.22        22.26 
TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       13.64         0.07        11.31        12.20        20.02         7.99 
TCGA-CG-4443 TCGA-CG-4475 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 TCGA-EQ-5647 
       29.98        22.98        15.02        20.55        15.22         0.62 
TCGA-EQ-8122 TCGA-FP-8211 TCGA-HU-8249 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 
        7.99        13.58        14.17        11.77        12.95        12.30 
TCGA-HU-A4HD TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
       27.42         1.41         6.44        37.64        45.67        18.21 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU 
       35.61         5.46        18.48        17.85        13.35        27.35 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       20.81        36.16        52.24         4.54        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       11.24        18.41        40.08        16.14        12.43         0.79 

$`DEL PEAK 35(12Q23.1) WILD-TYPE`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69         6.21        20.09         0.85        20.78        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       14.86         4.67        12.16       122.10        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
        6.28         3.16         0.30         4.31        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        4.70        19.99        47.93        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90        29.00         7.43         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.95        35.97        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37         8.71        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       52.57        46.09        10.36         5.92        10.45        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       15.52        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         5.16         8.02         7.59        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       29.59         6.35        53.95         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       12.69         7.00         5.29         4.80        15.35         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       28.11        30.71        18.18        46.19        15.06         9.17 
TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       15.91         3.42         2.10        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       12.82         9.21        24.76        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73        12.43         9.07        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49        14.43         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        16.31         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       19.17        14.79         0.26        15.85         3.72        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        12.43        11.61         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       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-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.40         7.13        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03         0.56         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        5.36         5.19        13.08         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF 
       60.56        20.15         3.72        19.73         9.86         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       61.25         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        18.74        22.68         1.71         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94U TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       64.18         2.66        22.09        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        21.11        10.62 

  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                         68.02                         122.30 
  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE 
                        13.445                         12.590 
[1] "0.1 - 68.0 (13.4)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(12Q23.1) MUTATED         4        4        6        3        14
  DEL PEAK 35(12Q23.1) WILD-TYPE       7       15       42       29        63
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(12Q23.1) MUTATED          18         4         18          9
  DEL PEAK 35(12Q23.1) WILD-TYPE        66        25         79         63
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(12Q23.1) MUTATED            9        6         1
  DEL PEAK 35(12Q23.1) WILD-TYPE         39       45         3
D74V3, multiclass
            clus
vv           DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              4                             15
  STAGE IB                              6                             42
  STAGE II                              3                             29
  STAGE IIA                            14                             63
  STAGE IIB                            18                             66
  STAGE III                             4                             25
  STAGE IIIA                           18                             79
  STAGE IIIB                            9                             63
  STAGE IIIC                            9                             39
  STAGE IV                              6                             45
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 35(12Q23.1) MUTATED      15  16  56  12
  DEL PEAK 35(12Q23.1) WILD-TYPE    38 110 224 112
D74V4, multiclass
       clus
vv      DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  T0+T1                           15                             38
  T2                              16                            110
  T3                              56                            224
  T4                              12                            112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 35(12Q23.1) MUTATED    35  32  17  14
  DEL PEAK 35(12Q23.1) WILD-TYPE 165 150  79  83
D74V5, multiclass
    clus
vv   DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  N0                           35                            165
  N1                           32                            150
  N2                           17                             79
  N3                           14                             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"
D74V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(12Q23.1) MUTATED    85   5
  DEL PEAK 35(12Q23.1) WILD-TYPE 428  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(12Q23.1) MUTATED     85    5
  DEL PEAK 35(12Q23.1) WILD-TYPE  428   34
   clus
vv  DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  0                           85                            428
  1                            5                             34
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(12Q23.1) MUTATED    32  72
  DEL PEAK 35(12Q23.1) WILD-TYPE 150 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(12Q23.1) MUTATED     32   72
  DEL PEAK 35(12Q23.1) WILD-TYPE  150  355
        clus
vv       DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  FEMALE                           32                            150
  MALE                             72                            355
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 35(12Q23.1) MUTATED                                       5
  DEL PEAK 35(12Q23.1) WILD-TYPE                                    66
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(12Q23.1) MUTATED                                                       19
  DEL PEAK 35(12Q23.1) WILD-TYPE                                                    143
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(12Q23.1) MUTATED                                                                  12
  DEL PEAK 35(12Q23.1) WILD-TYPE                                                                69
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 35(12Q23.1) MUTATED                                                 17
  DEL PEAK 35(12Q23.1) WILD-TYPE                                               61
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 35(12Q23.1) MUTATED                                                          1
  DEL PEAK 35(12Q23.1) WILD-TYPE                                                       20
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 35(12Q23.1) MUTATED                                                           1
  DEL PEAK 35(12Q23.1) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 35(12Q23.1) MUTATED                                          1
  DEL PEAK 35(12Q23.1) WILD-TYPE                                       12
D74V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 35(12Q23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 35(12Q23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       143
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(12Q23.1) MUTATED     0 104
  DEL PEAK 35(12Q23.1) WILD-TYPE   6 499
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(12Q23.1) MUTATED      0  104
  DEL PEAK 35(12Q23.1) WILD-TYPE    6  499
     clus
vv    DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  NO                             0                              6
  YES                          104                            499
[1] 2 2
[1] FALSE
D74V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(12Q23.1) MUTATED    45   3   2   2
  DEL PEAK 35(12Q23.1) WILD-TYPE 302  15  17  23
D74V11, multiclass
    clus
vv   DEL PEAK 35(12Q23.1) MUTATED DEL PEAK 35(12Q23.1) WILD-TYPE
  R0                           45                            302
  R1                            3                             15
  R2                            2                             17
  RX                            2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(12Q23.1) MUTATED      18                         3
  DEL PEAK 35(12Q23.1) WILD-TYPE   111                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(12Q23.1) MUTATED                                           0
  DEL PEAK 35(12Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 35(12Q23.1) MUTATED      68
  DEL PEAK 35(12Q23.1) WILD-TYPE   317
D74V13, multiclass
                                           clus
vv                                          DEL PEAK 35(12Q23.1) MUTATED
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               68
                                           clus
vv                                          DEL PEAK 35(12Q23.1) WILD-TYPE
  ASIAN                                                                111
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                                cls
clus                               0   1
  DEL PEAK 35(12Q23.1) MUTATED     1  53
  DEL PEAK 35(12Q23.1) WILD-TYPE   6 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(12Q23.1) MUTATED      1   53
  DEL PEAK 35(12Q23.1) WILD-TYPE    6  341
                        clus
vv                       DEL PEAK 35(12Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK 35(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            341
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 36(13Q12.11) MUTATION ANALYSIS
D75V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(13Q12.11) MUTATED    71  52
  DEL PEAK 36(13Q12.11) WILD-TYPE 283 169
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                            123                             452 
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                             52                             169 
$`DEL PEAK 36(13Q12.11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        58.55         7.63         8.94        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
        0.85        20.78         2.63         3.88        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93C 
       23.41         9.96         4.67        60.39        68.02        23.18 
TCGA-JY-A93E TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT 
       25.22         8.94         3.68        47.93         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW 
       29.00         6.94        13.22         5.49        83.24        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10        13.15        15.35        13.25        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HV 
       12.59        22.39         0.10        11.54        12.33        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.23        12.03         0.13         5.16         5.06        29.59 
TCGA-R6-A6XQ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP 
        6.35         1.45        12.69         4.80        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       22.82        18.31        28.11        30.71        18.18        42.87 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6456 
       11.24        15.91         2.10        19.56         6.97        17.29 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8289 
       26.10        12.16        15.42        28.01        18.71         2.66 
TCGA-BR-8297 TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-8526 
        7.40         9.86         1.48        12.89         0.66         0.07 
TCGA-CD-8527 TCGA-CD-A486 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 
        0.07         3.42        47.05        18.97        22.98        12.03 
TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6818 
       15.02        79.07        11.93        13.35        10.26        10.55 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 TCGA-HU-8243 TCGA-HU-A4GC 
       18.21        16.44        15.65        14.07         5.92         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 
       25.81        11.77         6.25        12.95        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-AB1X TCGA-RD-A7BS TCGA-RD-A8N1 
        5.36         5.19         6.74        13.51        11.05       115.69 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91Q 
       13.25        13.02         7.73         1.87        36.69        20.81 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-AA6G 
        4.54        64.18        26.04 

$`DEL PEAK 36(13Q12.11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        7.69         6.21        33.27        20.12        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        0.53        12.82        14.86        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       44.75         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        4.31        24.00         4.70        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
       18.35         3.32         7.17         1.38        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.43         8.71         2.60        25.12         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        3.95         3.02        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        27.12        52.57         0.10         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       12.59        15.52        12.33        13.22         4.47        25.25 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.00        13.18        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       14.70         7.04        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        7.00        20.02        20.38         5.29         3.42        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D 
        9.27         4.44        12.43         1.55         8.12        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       15.06         9.17        10.16         3.42         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        11.01         9.47         9.44         6.61 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
        9.21        24.76        35.24        23.93        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       28.73        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        16.31         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        22.26        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53        12.82        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        9.34        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        23.84        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        13.08         1.41         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.56         1.81         7.82         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       19.04         5.79         0.92        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       26.24        27.35        64.57        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.93        61.22        18.74        22.68         1.71        36.16 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        7.36         9.50         9.73        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       11.24        22.09        18.41        40.08        28.41        32.94 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       29.98        17.13        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       10.62         0.79 

  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE 
                          12.66                           12.79 
[1] "0.1 - 115.7 (12.7)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D75V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(13Q12.11) MUTATED         2        3       12        4        25
  DEL PEAK 36(13Q12.11) WILD-TYPE       9       16       36       28        52
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(13Q12.11) MUTATED          15        12         20         13
  DEL PEAK 36(13Q12.11) WILD-TYPE        69        17         77         59
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 36(13Q12.11) MUTATED            7        9         1
  DEL PEAK 36(13Q12.11) WILD-TYPE         41       42         3
D75V3, multiclass
            clus
vv           DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  STAGE I                                2                               9
  STAGE IA                               3                              16
  STAGE IB                              12                              36
  STAGE II                               4                              28
  STAGE IIA                             25                              52
  STAGE IIB                             15                              69
  STAGE III                             12                              17
  STAGE IIIA                            20                              77
  STAGE IIIB                            13                              59
  STAGE IIIC                             7                              41
  STAGE IV                               9                              42
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 36(13Q12.11) MUTATED      11  31  68  15
  DEL PEAK 36(13Q12.11) WILD-TYPE    42  95 212 109
D75V4, multiclass
       clus
vv      DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  T0+T1                            11                              42
  T2                               31                              95
  T3                               68                             212
  T4                               15                             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 36(13Q12.11) MUTATED    50  40  16  19
  DEL PEAK 36(13Q12.11) WILD-TYPE 150 142  80  78
D75V5, multiclass
    clus
vv   DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  N0                            50                             150
  N1                            40                             142
  N2                            16                              80
  N3                            19                              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"
D75V6, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q12.11) MUTATED   110   7
  DEL PEAK 36(13Q12.11) WILD-TYPE 403  32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q12.11) MUTATED    110    7
  DEL PEAK 36(13Q12.11) WILD-TYPE  403   32
   clus
vv  DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  0                           110                             403
  1                             7                              32
[1] 2 2
[1] FALSE
D75V7, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q12.11) MUTATED    21 110
  DEL PEAK 36(13Q12.11) WILD-TYPE 161 317
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q12.11) MUTATED     21  110
  DEL PEAK 36(13Q12.11) WILD-TYPE  161  317
        clus
vv       DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  FEMALE                            21                             161
  MALE                             110                             317
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 36(13Q12.11) MUTATED                                      12
  DEL PEAK 36(13Q12.11) WILD-TYPE                                    59
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(13Q12.11) MUTATED                                                       21
  DEL PEAK 36(13Q12.11) WILD-TYPE                                                    141
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(13Q12.11) MUTATED                                                                   8
  DEL PEAK 36(13Q12.11) WILD-TYPE                                                                73
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 36(13Q12.11) MUTATED                                                 12
  DEL PEAK 36(13Q12.11) WILD-TYPE                                               66
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 36(13Q12.11) MUTATED                                                          4
  DEL PEAK 36(13Q12.11) WILD-TYPE                                                       17
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 36(13Q12.11) MUTATED                                                           1
  DEL PEAK 36(13Q12.11) WILD-TYPE                                                         7
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 36(13Q12.11) MUTATED                                          2
  DEL PEAK 36(13Q12.11) WILD-TYPE                                       11
D75V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 36(13Q12.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      2
                                                                   clus
vv                                                                  DEL PEAK 36(13Q12.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              73
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               66
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       11
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q12.11) MUTATED     3 128
  DEL PEAK 36(13Q12.11) WILD-TYPE   3 475
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q12.11) MUTATED      3  128
  DEL PEAK 36(13Q12.11) WILD-TYPE    3  475
     clus
vv    DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  NO                              3                               3
  YES                           128                             475
[1] 2 2
[1] FALSE
D75V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 36(13Q12.11) MUTATED    47   4   3   4
  DEL PEAK 36(13Q12.11) WILD-TYPE 300  14  16  21
D75V11, multiclass
    clus
vv   DEL PEAK 36(13Q12.11) MUTATED DEL PEAK 36(13Q12.11) WILD-TYPE
  R0                            47                             300
  R1                             4                              14
  R2                             3                              16
  RX                             4                              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(13Q12.11) MUTATED      36                         1
  DEL PEAK 36(13Q12.11) WILD-TYPE    93                        12
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(13Q12.11) MUTATED                                           0
  DEL PEAK 36(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 36(13Q12.11) MUTATED      78
  DEL PEAK 36(13Q12.11) WILD-TYPE   307
D75V13, multiclass
                                           clus
vv                                          DEL PEAK 36(13Q12.11) MUTATED
  ASIAN                                                                36
  BLACK OR AFRICAN AMERICAN                                             1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                78
                                           clus
vv                                          DEL PEAK 36(13Q12.11) WILD-TYPE
  ASIAN                                                                  93
  BLACK OR AFRICAN AMERICAN                                              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q12.11) MUTATED     1  82
  DEL PEAK 36(13Q12.11) WILD-TYPE   6 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q12.11) MUTATED      1   82
  DEL PEAK 36(13Q12.11) WILD-TYPE    6  312
                        clus
vv                       DEL PEAK 36(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            82
                        clus
vv                       DEL PEAK 36(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             312
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 37(13Q14.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(13Q14.2) MUTATED    69  44
  DEL PEAK 37(13Q14.2) WILD-TYPE 285 177
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                           113                            462 
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                            44                            177 
$`DEL PEAK 37(13Q14.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IG-A3QL TCGA-IG-A3Y9 
       25.78        58.55         7.63         8.94        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93E 
        9.96        44.75        60.39        68.02         3.68        25.22 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU 
       24.00         3.68        21.01        47.93         3.16        29.00 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU 
        3.95         3.02        13.48        13.22         5.49        83.24 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       46.09        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A9FO 
       13.22        12.33        10.52        12.23        12.03         0.13 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO 
        5.06        29.59         6.35        12.69         4.80        18.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       19.96        22.82        18.31        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6564 
       42.87        15.91         6.61         6.97        17.29        26.10 
TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8297 TCGA-BR-A4CS TCGA-BR-A4IY 
       12.16        15.42        28.01         7.40         1.48        12.89 
TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A486 
        0.66         0.07         0.10         0.16         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5727 
        9.34        12.43         3.02        18.97        22.98        79.07 
TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8575 
       21.07        11.93        13.35        17.19        12.79        18.21 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 TCGA-FP-8211 TCGA-HU-A4GC 
       21.14        16.44        15.65        14.07        13.58         3.25 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
        6.25        12.95         3.45         3.39         5.36         5.19 
TCGA-IN-A6RR TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A925 
        6.74        11.05         7.73         1.87         4.54 

$`DEL PEAK 37(13Q14.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45         7.69         6.21        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       12.16       122.10        41.52        42.77        25.41        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       23.18        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI 
        0.30         4.31         8.94         4.70        32.61        19.99 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        0.36         7.40        55.50         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55         7.76        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 
       27.12        52.57         0.10        12.46        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 
       12.33         4.47        25.25        12.00        13.18        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
       53.95         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW 
       20.02        20.38         5.29         3.42        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G 
        4.44        12.43         1.55         8.12        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        10.16         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        9.44         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        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-7717 
       12.82         9.21        24.76        35.24        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         2.20        15.58         6.18        19.50        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         8.22        10.68        12.56        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        22.26        13.41        13.51         8.98         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-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         0.13         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.10        11.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        69.04         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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.85        10.26        15.22        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34         7.40         7.13         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        5.52         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-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-A4H3 
        0.10         6.51        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       21.21        18.81        18.38        13.08         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        0.92        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       26.24        27.35        64.57        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        36.16         7.36         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        64.18 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 
       21.04         2.66        42.54        11.24        22.09        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       40.08        28.41        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        21.11        12.43        10.62         0.79 

  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE 
                         12.59                          12.82 
[1] "0.1 - 83.2 (12.6)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(13Q14.2) MUTATED         4        2        7        4        23
  DEL PEAK 37(13Q14.2) WILD-TYPE       7       17       41       28        54
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(13Q14.2) MUTATED          17        15         22          8
  DEL PEAK 37(13Q14.2) WILD-TYPE        67        14         75         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 37(13Q14.2) MUTATED            5        4         1
  DEL PEAK 37(13Q14.2) WILD-TYPE         43       47         3
D76V3, multiclass
            clus
vv           DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              2                             17
  STAGE IB                              7                             41
  STAGE II                              4                             28
  STAGE IIA                            23                             54
  STAGE IIB                            17                             67
  STAGE III                            15                             14
  STAGE IIIA                           22                             75
  STAGE IIIB                            8                             64
  STAGE IIIC                            5                             43
  STAGE IV                              4                             47
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 37(13Q14.2) MUTATED      12  27  64  11
  DEL PEAK 37(13Q14.2) WILD-TYPE    41  99 216 113
D76V4, multiclass
       clus
vv      DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  T0+T1                           12                             41
  T2                              27                             99
  T3                              64                            216
  T4                              11                            113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 37(13Q14.2) MUTATED    47  43  12  12
  DEL PEAK 37(13Q14.2) WILD-TYPE 153 139  84  85
D76V5, multiclass
    clus
vv   DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  N0                           47                            153
  N1                           43                            139
  N2                           12                             84
  N3                           12                             85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(13Q14.2) MUTATED   102   4
  DEL PEAK 37(13Q14.2) WILD-TYPE 411  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(13Q14.2) MUTATED    102    4
  DEL PEAK 37(13Q14.2) WILD-TYPE  411   35
   clus
vv  DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  0                          102                            411
  1                            4                             35
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(13Q14.2) MUTATED    22  97
  DEL PEAK 37(13Q14.2) WILD-TYPE 160 330
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(13Q14.2) MUTATED     22   97
  DEL PEAK 37(13Q14.2) WILD-TYPE  160  330
        clus
vv       DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  FEMALE                           22                            160
  MALE                             97                            330
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 37(13Q14.2) MUTATED                                      10
  DEL PEAK 37(13Q14.2) WILD-TYPE                                    61
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(13Q14.2) MUTATED                                                       23
  DEL PEAK 37(13Q14.2) WILD-TYPE                                                    139
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(13Q14.2) MUTATED                                                                   5
  DEL PEAK 37(13Q14.2) WILD-TYPE                                                                76
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 37(13Q14.2) MUTATED                                                  8
  DEL PEAK 37(13Q14.2) WILD-TYPE                                               70
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 37(13Q14.2) MUTATED                                                          2
  DEL PEAK 37(13Q14.2) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 37(13Q14.2) MUTATED                                                           0
  DEL PEAK 37(13Q14.2) WILD-TYPE                                                         8
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 37(13Q14.2) MUTATED                                          1
  DEL PEAK 37(13Q14.2) WILD-TYPE                                       12
D76V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 37(13Q14.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 37(13Q14.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             76
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              70
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(13Q14.2) MUTATED     3 116
  DEL PEAK 37(13Q14.2) WILD-TYPE   3 487
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(13Q14.2) MUTATED      3  116
  DEL PEAK 37(13Q14.2) WILD-TYPE    3  487
     clus
vv    DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  NO                             3                              3
  YES                          116                            487
[1] 2 2
[1] FALSE
D76V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(13Q14.2) MUTATED    35   4   2   5
  DEL PEAK 37(13Q14.2) WILD-TYPE 312  14  17  20
D76V11, multiclass
    clus
vv   DEL PEAK 37(13Q14.2) MUTATED DEL PEAK 37(13Q14.2) WILD-TYPE
  R0                           35                            312
  R1                            4                             14
  R2                            2                             17
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(13Q14.2) MUTATED      38                         0
  DEL PEAK 37(13Q14.2) WILD-TYPE    91                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(13Q14.2) MUTATED                                           0
  DEL PEAK 37(13Q14.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 37(13Q14.2) MUTATED      69
  DEL PEAK 37(13Q14.2) WILD-TYPE   316
D76V13, multiclass
                                           clus
vv                                          DEL PEAK 37(13Q14.2) MUTATED
  ASIAN                                                               38
  BLACK OR AFRICAN AMERICAN                                            0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               69
                                           clus
vv                                          DEL PEAK 37(13Q14.2) WILD-TYPE
  ASIAN                                                                 91
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                                cls
clus                               0   1
  DEL PEAK 37(13Q14.2) MUTATED     1  76
  DEL PEAK 37(13Q14.2) WILD-TYPE   6 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(13Q14.2) MUTATED      1   76
  DEL PEAK 37(13Q14.2) WILD-TYPE    6  318
                        clus
vv                       DEL PEAK 37(13Q14.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       DEL PEAK 37(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            318
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 38(13Q21.31) MUTATION ANALYSIS
D77V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 38(13Q21.31) MUTATED    68  47
  DEL PEAK 38(13Q21.31) WILD-TYPE 286 174
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                            115                             460 
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                             47                             174 
$`DEL PEAK 38(13Q21.31) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 
       58.55         7.63         8.94        32.45        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       20.78         2.63         3.88         0.53        17.03        23.41 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OE 
        9.96        44.75        60.39        68.02        25.22        24.00 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V 
        3.68        21.01        47.93         3.16        29.00         2.60 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.48        13.22         5.49        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       15.35        13.25        12.46        12.49        12.76        22.39 
TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY 
        0.10        13.22        12.33        10.52        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WG 
        0.13         7.59         5.06         6.35         9.30        12.69 
TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX 
        4.80        18.81        19.96        22.82        18.31        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6564 
       18.18        42.87        15.91         6.61         6.97        26.10 
TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-8297 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CS 
       12.16        28.01         7.40        20.22         9.86         1.48 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.89         0.66         0.07         0.07         0.10         0.16 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-4475 
        3.42         9.34         3.02        47.05        18.97        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6520 TCGA-D7-6525 
       30.97        36.00        79.07        21.07        18.84        13.35 
TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       17.19        12.79        18.21        14.66        21.14        16.44 
TCGA-D7-A4YY TCGA-D7-A74A TCGA-FP-7916 TCGA-FP-8211 TCGA-HU-A4GC TCGA-HU-A4H2 
       13.78         7.40        14.07        13.58         3.25        12.95 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RR TCGA-RD-A7BS 
        3.45        18.81         5.36         1.41         6.74        11.05 
TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A925 TCGA-VQ-AA6A TCGA-VQ-AA6F 
        7.73         1.87        36.69         4.54        32.94        54.12 
TCGA-VQ-AA6I 
       16.14 

$`DEL PEAK 38(13Q21.31) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       25.78        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 
        4.21         7.69         6.21        33.27        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        9.30         0.79        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 
       12.16       122.10         3.68        41.52        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        31.56        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         0.30         4.31         8.94         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       19.99        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        4.90         7.13         7.43         6.94         8.71        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        0.36         7.40         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49V 
        8.71        13.41        27.12        52.57        12.66         0.10 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
        0.10        12.59        12.59        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
        4.47        25.25        12.00        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.82         8.02        14.70         7.04        29.59        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         2.89         1.45         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER 
        5.29         3.42        15.35         9.27         4.44        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        1.55         8.12        30.71        46.19        15.06        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        10.16         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        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-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       22.26        13.41        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82        19.36        13.51         0.46        20.65 
TCGA-BR-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-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.13         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
       20.55        18.54        18.61        17.85        10.26        15.22 
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-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        17.19        20.91        14.27         5.92        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.81        27.42        21.21         3.39        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.08         6.44        12.59         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        7.82        13.51         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
        8.52        61.25         6.08         4.60         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48        28.96        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.68         1.71        36.16         7.36         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
       64.18        21.04         2.66        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        40.08        28.41        29.98        17.13        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                          83.24                          122.30 
  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE 
                          12.95                           12.64 
[1] "0.1 - 83.2 (12.9)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D77V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(13Q21.31) MUTATED         3        4        7        5        19
  DEL PEAK 38(13Q21.31) WILD-TYPE       8       15       41       27        58
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(13Q21.31) MUTATED          16        13         23         13
  DEL PEAK 38(13Q21.31) WILD-TYPE        68        16         74         59
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 38(13Q21.31) MUTATED            6        4         1
  DEL PEAK 38(13Q21.31) WILD-TYPE         42       47         3
D77V3, multiclass
            clus
vv           DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  STAGE I                                3                               8
  STAGE IA                               4                              15
  STAGE IB                               7                              41
  STAGE II                               5                              27
  STAGE IIA                             19                              58
  STAGE IIB                             16                              68
  STAGE III                             13                              16
  STAGE IIIA                            23                              74
  STAGE IIIB                            13                              59
  STAGE IIIC                             6                              42
  STAGE IV                               4                              47
  STAGE IVA                              1                               3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 38(13Q21.31) MUTATED      13  28  61  13
  DEL PEAK 38(13Q21.31) WILD-TYPE    40  98 219 111
D77V4, multiclass
       clus
vv      DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  T0+T1                            13                              40
  T2                               28                              98
  T3                               61                             219
  T4                               13                             111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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(13Q21.31) MUTATED    43  40  14  17
  DEL PEAK 38(13Q21.31) WILD-TYPE 157 142  82  80
D77V5, multiclass
    clus
vv   DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  N0                            43                             157
  N1                            40                             142
  N2                            14                              82
  N3                            17                              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"
D77V6, binary
                                 cls
clus                                0   1
  DEL PEAK 38(13Q21.31) MUTATED   101   4
  DEL PEAK 38(13Q21.31) WILD-TYPE 412  35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(13Q21.31) MUTATED    101    4
  DEL PEAK 38(13Q21.31) WILD-TYPE  412   35
   clus
vv  DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  0                           101                             412
  1                             4                              35
[1] 2 2
[1] FALSE
D77V7, binary
                                 cls
clus                                0   1
  DEL PEAK 38(13Q21.31) MUTATED    26  94
  DEL PEAK 38(13Q21.31) WILD-TYPE 156 333
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(13Q21.31) MUTATED     26   94
  DEL PEAK 38(13Q21.31) WILD-TYPE  156  333
        clus
vv       DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  FEMALE                            26                             156
  MALE                              94                             333
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 38(13Q21.31) MUTATED                                      10
  DEL PEAK 38(13Q21.31) WILD-TYPE                                    61
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(13Q21.31) MUTATED                                                       20
  DEL PEAK 38(13Q21.31) WILD-TYPE                                                    142
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(13Q21.31) MUTATED                                                                  11
  DEL PEAK 38(13Q21.31) WILD-TYPE                                                                70
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 38(13Q21.31) MUTATED                                                 11
  DEL PEAK 38(13Q21.31) WILD-TYPE                                               67
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 38(13Q21.31) MUTATED                                                          2
  DEL PEAK 38(13Q21.31) WILD-TYPE                                                       19
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 38(13Q21.31) MUTATED                                                           0
  DEL PEAK 38(13Q21.31) WILD-TYPE                                                         8
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 38(13Q21.31) MUTATED                                          1
  DEL PEAK 38(13Q21.31) WILD-TYPE                                       12
D77V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 38(13Q21.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  DEL PEAK 38(13Q21.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                                 cls
clus                                0   1
  DEL PEAK 38(13Q21.31) MUTATED     3 117
  DEL PEAK 38(13Q21.31) WILD-TYPE   3 486
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(13Q21.31) MUTATED      3  117
  DEL PEAK 38(13Q21.31) WILD-TYPE    3  486
     clus
vv    DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  NO                              3                               3
  YES                           117                             486
[1] 2 2
[1] FALSE
D77V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 38(13Q21.31) MUTATED    44   3   2   4
  DEL PEAK 38(13Q21.31) WILD-TYPE 303  15  17  21
D77V11, multiclass
    clus
vv   DEL PEAK 38(13Q21.31) MUTATED DEL PEAK 38(13Q21.31) WILD-TYPE
  R0                            44                             303
  R1                             3                              15
  R2                             2                              17
  RX                             4                              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(13Q21.31) MUTATED      35                         0
  DEL PEAK 38(13Q21.31) WILD-TYPE    94                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 38(13Q21.31) MUTATED                                           0
  DEL PEAK 38(13Q21.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 38(13Q21.31) MUTATED      70
  DEL PEAK 38(13Q21.31) WILD-TYPE   315
D77V13, multiclass
                                           clus
vv                                          DEL PEAK 38(13Q21.31) MUTATED
  ASIAN                                                                35
  BLACK OR AFRICAN AMERICAN                                             0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                70
                                           clus
vv                                          DEL PEAK 38(13Q21.31) WILD-TYPE
  ASIAN                                                                  94
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                                 cls
clus                                0   1
  DEL PEAK 38(13Q21.31) MUTATED     2  72
  DEL PEAK 38(13Q21.31) WILD-TYPE   5 322
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(13Q21.31) MUTATED      2   72
  DEL PEAK 38(13Q21.31) WILD-TYPE    5  322
                        clus
vv                       DEL PEAK 38(13Q21.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            72
                        clus
vv                       DEL PEAK 38(13Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             322
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 39(14Q23.3) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(14Q23.3) MUTATED   101  74
  DEL PEAK 39(14Q23.3) WILD-TYPE 253 147
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                           175                            400 
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                            74                            147 
$`DEL PEAK 39(14Q23.3) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL 
       31.27         7.63         8.94        16.24         4.21        20.09 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FB 
       23.41        12.82         4.67        14.50       122.10        60.39 
TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.22         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y 
        4.70         3.16        29.00         7.13         6.94         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
        3.95        55.50         2.66        16.47        10.36        10.45 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6DQ 
       13.25        12.59        10.52        12.03        33.11         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO 
        5.06         6.35         9.30        15.78         7.00        18.81 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN 
       22.82        12.43        18.31        42.87        15.06         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4279 
       19.73        19.56        11.01         9.44         6.61         9.57 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 
       17.29        19.33        26.10         9.17        31.20        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
       15.42        28.01        28.73        18.71        17.49        11.44 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       12.95         2.66        19.50        14.79         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 
       25.18         9.21        15.81        11.54        15.68         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       22.26         1.48         0.72         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 
       20.65         1.15        13.18         0.07         0.07         0.07 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.13         0.13        11.31        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4477 
        8.05        54.08         4.01        14.01        18.97        30.97 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       15.02        20.55        18.84        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6EY 
       10.26        15.98        14.66        16.44        11.31        11.44 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
        2.96         7.99        16.24        11.38        14.07        17.06 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G3 TCGA-HU-A4GC 
        0.56        26.47        12.59        14.17         5.59         3.25 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 
       11.77         8.98         2.10        12.30        27.42        21.21 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 
        5.19        13.08         6.44         6.74         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
        5.56        37.64        16.67       122.30        37.91       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         0.92         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       35.24        32.48         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       17.85        13.35        27.35        64.57        14.33        65.16 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O 
       18.74        20.81        52.24         9.04        64.18        21.04 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G 
       42.54        22.09        18.41        32.94        29.98        26.04 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 39(14Q23.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR 
       25.78        14.30        58.55         5.92        13.94        32.45 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.12        18.64         3.88         9.30         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        0.79         9.96        14.86        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        25.41        21.70        23.18        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         4.31        32.61 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V 
        1.38        58.59         4.90         7.43         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
       25.12         7.40         3.02        35.97        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K 
       13.41        27.12        83.24        52.57        46.09         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41         0.10        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10         0.10        12.46        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        12.00        12.23        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         5.16         7.82         8.02        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
       29.59        53.95         2.89         1.45        12.69        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        4.44        19.96         1.55         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       18.18        46.19        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 
        3.42         2.10        26.70        11.70         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
        4.64         7.43        18.35        30.90         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 
       34.68        15.95        13.87        13.68        39.12        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        12.43         3.45         9.07        12.76 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        16.31         2.20        15.58         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 
        4.31        14.04         3.32        11.80        19.17        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        3.72        20.22         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        12.56        13.87         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
        3.25        13.15         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         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        9.34        12.43        11.61         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4444 
        3.02        27.02        15.95         1.02        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       12.66        11.93        19.13        18.61        17.85        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-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76        15.65         8.38         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        0.62        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       22.29        59.54         5.03        13.58         5.52         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08         1.51         5.92        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       22.75        25.81        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       18.38         5.36         1.41        12.59         6.51         5.56 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ 
        7.82        13.51        60.56        20.15         3.72        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 
        4.60         9.24        11.05         8.61         5.13        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 
        5.79        48.79        21.73        34.45        27.88        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO 
       34.29        16.31        22.19         2.50         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        26.24        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        11.24        40.08        28.41        17.13        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        21.11        12.43        10.62 

  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE 
                        13.250                         12.575 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(14Q23.3) MUTATED         3        3       13       11        21
  DEL PEAK 39(14Q23.3) WILD-TYPE       8       16       35       21        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(14Q23.3) MUTATED          24         9         36         25
  DEL PEAK 39(14Q23.3) WILD-TYPE        60        20         61         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 39(14Q23.3) MUTATED           14       10         3
  DEL PEAK 39(14Q23.3) WILD-TYPE         34       41         1
D78V3, multiclass
            clus
vv           DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  STAGE I                               3                              8
  STAGE IA                              3                             16
  STAGE IB                             13                             35
  STAGE II                             11                             21
  STAGE IIA                            21                             56
  STAGE IIB                            24                             60
  STAGE III                             9                             20
  STAGE IIIA                           36                             61
  STAGE IIIB                           25                             47
  STAGE IIIC                           14                             34
  STAGE IV                             10                             41
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 39(14Q23.3) MUTATED      14  33  91  37
  DEL PEAK 39(14Q23.3) WILD-TYPE    39  93 189  87
D78V4, multiclass
       clus
vv      DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  T0+T1                           14                             39
  T2                              33                             93
  T3                              91                            189
  T4                              37                             87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 39(14Q23.3) MUTATED    53  56  39  24
  DEL PEAK 39(14Q23.3) WILD-TYPE 147 126  57  73
D78V5, multiclass
    clus
vv   DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  N0                           53                            147
  N1                           56                            126
  N2                           39                             57
  N3                           24                             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"
D78V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(14Q23.3) MUTATED   154   8
  DEL PEAK 39(14Q23.3) WILD-TYPE 359  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(14Q23.3) MUTATED    154    8
  DEL PEAK 39(14Q23.3) WILD-TYPE  359   31
   clus
vv  DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  0                          154                            359
  1                            8                             31
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(14Q23.3) MUTATED    51 132
  DEL PEAK 39(14Q23.3) WILD-TYPE 131 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(14Q23.3) MUTATED     51  132
  DEL PEAK 39(14Q23.3) WILD-TYPE  131  295
        clus
vv       DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  FEMALE                           51                            131
  MALE                            132                            295
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 39(14Q23.3) MUTATED                                      15
  DEL PEAK 39(14Q23.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(14Q23.3) MUTATED                                                       48
  DEL PEAK 39(14Q23.3) WILD-TYPE                                                    114
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(14Q23.3) MUTATED                                                                  34
  DEL PEAK 39(14Q23.3) WILD-TYPE                                                                47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 39(14Q23.3) MUTATED                                                 27
  DEL PEAK 39(14Q23.3) WILD-TYPE                                               51
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 39(14Q23.3) MUTATED                                                          2
  DEL PEAK 39(14Q23.3) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 39(14Q23.3) MUTATED                                                           3
  DEL PEAK 39(14Q23.3) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 39(14Q23.3) MUTATED                                          5
  DEL PEAK 39(14Q23.3) WILD-TYPE                                        8
D78V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 39(14Q23.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      48
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 39(14Q23.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       114
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(14Q23.3) MUTATED     1 182
  DEL PEAK 39(14Q23.3) WILD-TYPE   5 421
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(14Q23.3) MUTATED      1  182
  DEL PEAK 39(14Q23.3) WILD-TYPE    5  421
     clus
vv    DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  NO                             1                              5
  YES                          182                            421
[1] 2 2
[1] FALSE
D78V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(14Q23.3) MUTATED   114   2   3   7
  DEL PEAK 39(14Q23.3) WILD-TYPE 233  16  16  18
D78V11, multiclass
    clus
vv   DEL PEAK 39(14Q23.3) MUTATED DEL PEAK 39(14Q23.3) WILD-TYPE
  R0                          114                            233
  R1                            2                             16
  R2                            3                             16
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(14Q23.3) MUTATED      34                         3
  DEL PEAK 39(14Q23.3) WILD-TYPE    95                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 39(14Q23.3) MUTATED                                           0
  DEL PEAK 39(14Q23.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 39(14Q23.3) MUTATED     121
  DEL PEAK 39(14Q23.3) WILD-TYPE   264
D78V13, multiclass
                                           clus
vv                                          DEL PEAK 39(14Q23.3) MUTATED
  ASIAN                                                               34
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              121
                                           clus
vv                                          DEL PEAK 39(14Q23.3) WILD-TYPE
  ASIAN                                                                 95
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(14Q23.3) MUTATED     1 110
  DEL PEAK 39(14Q23.3) WILD-TYPE   6 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(14Q23.3) MUTATED      1  110
  DEL PEAK 39(14Q23.3) WILD-TYPE    6  284
                        clus
vv                       DEL PEAK 39(14Q23.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 39(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            284
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 40(14Q32.32) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(14Q32.32) MUTATED   108  70
  DEL PEAK 40(14Q32.32) WILD-TYPE 246 151
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                            178                             397 
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                             70                             151 
$`DEL PEAK 40(14Q32.32) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
        7.63         8.94        16.24         4.21        32.45        20.09 
TCGA-IG-A4P3 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       18.64        23.41        12.82         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M 
       44.75        60.39        42.77        25.22         0.30         8.94 
TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OU 
       24.00         3.68         4.70        32.61         3.16        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.13         6.94         0.36         3.95        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NN TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W 
       13.48        16.47         5.49        10.36        10.45        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 
       12.59        22.39        10.52        12.03         0.13        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-RE-A7BO 
        7.59         5.06        29.59         6.35         2.89         7.00 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-A8JE 
       18.81        22.82        18.18        42.87        15.06         2.10 
TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4279 
        2.66        19.56        11.01         6.61        18.35         9.57 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 
       17.29        19.33        26.10         9.17        12.16        31.20 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
       35.24        15.42        28.01        18.71        17.49        11.44 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 
        9.60        12.95         2.66        19.50        14.79         0.26 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 
        5.39        25.18         9.21        15.81        11.54        15.68 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 
       10.68         7.53         1.48        12.89         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-A48C 
        0.07         0.07         0.13         0.13        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
       12.20        20.02         7.99        54.08        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       19.07        30.97        21.07        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       13.35        10.26        15.98        14.66        14.27        16.44 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
       13.78        11.31         9.76         2.96         7.40         7.99 
TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 
       16.24        11.38        14.07        17.06         0.56        26.47 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 
       12.59        14.17        11.77         8.98         2.10        12.30 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       27.42        21.21        18.81         5.19         6.44         6.74 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        1.81         2.53        37.64        16.67       122.30        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        8.94        35.61         5.46        13.02        35.24         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ 
       46.26        12.79        13.35        27.35        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z 
       36.69        18.74        20.81        22.68         9.73        52.24 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94U TCGA-VQ-AA64 
        4.54         5.72        64.18        21.04        22.09        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       32.94        29.98        26.04         0.79 

$`DEL PEAK 40(14Q32.32) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         5.92        13.94 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.12         3.88         9.30         0.53        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        9.96        14.86        12.16        68.02         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       25.41        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         4.31        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         7.17         1.38        58.59         4.90 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.43         8.71         2.60        25.12         7.40         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       35.97        12.92        13.55        13.22         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        8.71        13.41        27.12        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35         0.10         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
        4.47        12.33        25.25        12.00        12.23        13.18 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        5.16         7.82         8.02        14.70         7.04        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
        9.30        15.78         1.45        12.69        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       19.96        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        46.19        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN 
        3.42        19.73        26.70        11.70         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 
       34.68        15.95        13.87        13.68        39.12        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82         9.21        24.76        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43         0.69        12.26        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
       16.31         2.20        15.58         7.40         6.18        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 
       14.04         3.32        11.80        19.17        15.85         3.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        12.79         9.34        13.45         6.28 
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         9.86         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       12.56        13.87         6.08        22.26        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE 
        8.98        14.17         0.53        12.82        13.51        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.30         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.10         0.10         3.42         9.34        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
        1.02         8.05         4.01        14.01        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        69.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 
       19.13        18.61        17.85        17.19        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19        18.21        21.14        20.91         5.92        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        13.71        11.24        11.44        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         0.62        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        5.52         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        12.95        19.36        23.84         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.81         3.45         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
        1.41        12.59         6.51         5.56         7.82        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
        9.24        11.05         8.61         5.13        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.25        18.48        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       27.88        32.48        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        26.24        14.33        11.70        11.93        61.22 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        36.16         7.36         9.50         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
       55.43         6.58         2.66        42.54        11.24        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        17.13        54.12        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE 
                          13.35                           12.56 
[1] "0.1 - 122.3 (13.3)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D79V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(14Q32.32) MUTATED         4        4       10       12        23
  DEL PEAK 40(14Q32.32) WILD-TYPE       7       15       38       20        54
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(14Q32.32) MUTATED          26        10         37         24
  DEL PEAK 40(14Q32.32) WILD-TYPE        58        19         60         48
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 40(14Q32.32) MUTATED           15        7         2
  DEL PEAK 40(14Q32.32) WILD-TYPE         33       44         2
D79V3, multiclass
            clus
vv           DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  STAGE I                                4                               7
  STAGE IA                               4                              15
  STAGE IB                              10                              38
  STAGE II                              12                              20
  STAGE IIA                             23                              54
  STAGE IIB                             26                              58
  STAGE III                             10                              19
  STAGE IIIA                            37                              60
  STAGE IIIB                            24                              48
  STAGE IIIC                            15                              33
  STAGE IV                               7                              44
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 40(14Q32.32) MUTATED      13  38  93  33
  DEL PEAK 40(14Q32.32) WILD-TYPE    40  88 187  91
D79V4, multiclass
       clus
vv      DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  T0+T1                            13                              40
  T2                               38                              88
  T3                               93                             187
  T4                               33                              91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 40(14Q32.32) MUTATED    55  59  34  28
  DEL PEAK 40(14Q32.32) WILD-TYPE 145 123  62  69
D79V5, multiclass
    clus
vv   DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  N0                            55                             145
  N1                            59                             123
  N2                            34                              62
  N3                            28                              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"
D79V6, binary
                                 cls
clus                                0   1
  DEL PEAK 40(14Q32.32) MUTATED   161   4
  DEL PEAK 40(14Q32.32) WILD-TYPE 352  35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(14Q32.32) MUTATED    161    4
  DEL PEAK 40(14Q32.32) WILD-TYPE  352   35
   clus
vv  DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  0                           161                             352
  1                             4                              35
[1] 2 2
[1] FALSE
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(14Q32.32) MUTATED    52 134
  DEL PEAK 40(14Q32.32) WILD-TYPE 130 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(14Q32.32) MUTATED     52  134
  DEL PEAK 40(14Q32.32) WILD-TYPE  130  293
        clus
vv       DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  FEMALE                            52                             130
  MALE                             134                             293
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 40(14Q32.32) MUTATED                                      15
  DEL PEAK 40(14Q32.32) WILD-TYPE                                    56
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(14Q32.32) MUTATED                                                       49
  DEL PEAK 40(14Q32.32) WILD-TYPE                                                    113
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(14Q32.32) MUTATED                                                                  28
  DEL PEAK 40(14Q32.32) WILD-TYPE                                                                53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 40(14Q32.32) MUTATED                                                 24
  DEL PEAK 40(14Q32.32) WILD-TYPE                                               54
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 40(14Q32.32) MUTATED                                                          6
  DEL PEAK 40(14Q32.32) WILD-TYPE                                                       15
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 40(14Q32.32) MUTATED                                                           4
  DEL PEAK 40(14Q32.32) WILD-TYPE                                                         4
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 40(14Q32.32) MUTATED                                          5
  DEL PEAK 40(14Q32.32) WILD-TYPE                                        8
D79V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 40(14Q32.32) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      5
                                                                   clus
vv                                                                  DEL PEAK 40(14Q32.32) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        113
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                                 cls
clus                                0   1
  DEL PEAK 40(14Q32.32) MUTATED     2 184
  DEL PEAK 40(14Q32.32) WILD-TYPE   4 419
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(14Q32.32) MUTATED      2  184
  DEL PEAK 40(14Q32.32) WILD-TYPE    4  419
     clus
vv    DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  NO                              2                               4
  YES                           184                             419
[1] 2 2
[1] FALSE
D79V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 40(14Q32.32) MUTATED   110   3   3   7
  DEL PEAK 40(14Q32.32) WILD-TYPE 237  15  16  18
D79V11, multiclass
    clus
vv   DEL PEAK 40(14Q32.32) MUTATED DEL PEAK 40(14Q32.32) WILD-TYPE
  R0                           110                             237
  R1                             3                              15
  R2                             3                              16
  RX                             7                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(14Q32.32) MUTATED      38                         3
  DEL PEAK 40(14Q32.32) WILD-TYPE    91                        10
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 40(14Q32.32) MUTATED                                           0
  DEL PEAK 40(14Q32.32) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 40(14Q32.32) MUTATED     124
  DEL PEAK 40(14Q32.32) WILD-TYPE   261
D79V13, multiclass
                                           clus
vv                                          DEL PEAK 40(14Q32.32) MUTATED
  ASIAN                                                                38
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               124
                                           clus
vv                                          DEL PEAK 40(14Q32.32) WILD-TYPE
  ASIAN                                                                  91
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                                 cls
clus                                0   1
  DEL PEAK 40(14Q32.32) MUTATED     0 116
  DEL PEAK 40(14Q32.32) WILD-TYPE   7 278
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(14Q32.32) MUTATED      0  116
  DEL PEAK 40(14Q32.32) WILD-TYPE    7  278
                        clus
vv                       DEL PEAK 40(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                           116
                        clus
vv                       DEL PEAK 40(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             278
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 41(15Q11.2) MUTATION ANALYSIS
D80V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(15Q11.2) MUTATED   105  62
  DEL PEAK 41(15Q11.2) WILD-TYPE 249 159
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                           167                            408 
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                            62                            159 
$`DEL PEAK 41(15Q11.2) MUTATED`
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
        7.63         5.92        16.24        32.45         7.69        20.09 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A938 TCGA-JY-A93C 
       20.12         3.88        12.82        14.50        25.41        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       31.56        25.22         0.30         8.94        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NE 
       32.61        47.93         4.90        29.00         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT 
        2.66        12.92         5.49         8.71        13.41        27.12 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A8 
       83.24        10.45         0.10        12.59        22.39        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-Q9-A6FU 
       12.33        12.33        25.25        12.03         0.13         5.16 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO 
        7.59         5.06        14.70        29.59         9.30         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EX 
       20.02        20.38         3.42         4.80        18.81        28.11 
TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-6457 
       18.18        10.16         3.42         2.10        11.01        13.68 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8286 
       19.33         9.17        24.76        35.24         3.45        12.95 
TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-8690 
        2.66        14.79         5.39         9.21        15.68        10.68 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8525 
       22.26         0.72        20.65        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A 
        0.07         0.07         0.13         0.16         0.13        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
       11.61        12.20        20.02         7.99        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 
       47.05        18.97         1.02        12.03        15.02        69.04 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 
       12.66        19.13        20.55        18.84        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 
       10.26        15.22        15.98        12.79        18.21        14.66 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 
       11.31         2.96        15.65         7.40         7.99        72.23 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 
       13.58         5.52         0.23        26.47        12.59        14.17 
TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       12.10         3.25        25.81        11.77         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ 
        2.10        23.84         9.67        27.42        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 
        5.19         1.41         5.56         1.81         2.53        60.56 
TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW 
        9.86         8.52         9.24        11.05        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
      115.69        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q 
       34.45        17.85        13.35        65.16        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94R 
        1.71         9.50         9.73        52.24        64.18        42.54 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       22.09        40.08        29.98        54.12        16.14 

$`DEL PEAK 41(15Q11.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN 
       25.78        31.27        14.30        58.55        13.94         8.94 
TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21         6.21        33.27         0.85        20.78         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       60.39        68.02         3.68        41.52        42.77        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         4.31         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       19.99        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        3.16        58.59         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
        2.60        25.12         0.36         7.40         3.95        35.97 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       13.48        16.47        13.55        13.22         7.76        21.37 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.46        12.49        12.76        12.59         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22         4.47        10.52        12.00        12.23        13.18 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
       33.11         7.82         8.02         7.04         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASV 
       15.78         2.89         1.45        12.69         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        19.96        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       11.24         9.17        15.91         2.66        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        4.64         7.43        18.35        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        17.29        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        23.93        15.42        28.01        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       19.17         0.26        15.85         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         9.86 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        8.22        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        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         3.42         9.34        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        8.05        14.01        29.98        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
       12.36        11.93        18.54        18.61        17.85        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-D7-8578 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-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         0.62        16.24        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8238 
       17.06        59.54         5.03         0.56        18.08         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-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ 
        5.59        12.30        11.84        24.20        22.75        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
       29.98         0.10         6.51        10.19         0.26        12.95 
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-8663 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         3.39        13.08         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H 
        6.51         7.82        13.51         5.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        45.67        18.21        61.25         6.08 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        4.60         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV 
       71.38        57.44         8.94        16.87        19.04        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        18.48        35.24        21.73        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
        7.73        28.96        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
       15.65        26.24        27.35        64.57        14.33        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        11.93        61.22        22.68        36.16         7.36 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       21.04         2.66        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        21.11        12.43        10.62         0.79 

  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE 
                        12.820                         12.725 
[1] "0.1 - 115.7 (12.8)" "0.0 - 122.3 (12.7)"
[1] "hr=" "1.1"
D80V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(15Q11.2) MUTATED         4        5       14        7        21
  DEL PEAK 41(15Q11.2) WILD-TYPE       7       14       34       25        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(15Q11.2) MUTATED          23         8         37         20
  DEL PEAK 41(15Q11.2) WILD-TYPE        61        21         60         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 41(15Q11.2) MUTATED            9       15         3
  DEL PEAK 41(15Q11.2) WILD-TYPE         39       36         1
D80V3, multiclass
            clus
vv           DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              5                             14
  STAGE IB                             14                             34
  STAGE II                              7                             25
  STAGE IIA                            21                             56
  STAGE IIB                            23                             61
  STAGE III                             8                             21
  STAGE IIIA                           37                             60
  STAGE IIIB                           20                             52
  STAGE IIIC                            9                             39
  STAGE IV                             15                             36
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 41(15Q11.2) MUTATED      17  38  92  22
  DEL PEAK 41(15Q11.2) WILD-TYPE    36  88 188 102
D80V4, multiclass
       clus
vv      DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  T0+T1                           17                             36
  T2                              38                             88
  T3                              92                            188
  T4                              22                            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 41(15Q11.2) MUTATED    58  52  33  23
  DEL PEAK 41(15Q11.2) WILD-TYPE 142 130  63  74
D80V5, multiclass
    clus
vv   DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  N0                           58                            142
  N1                           52                            130
  N2                           33                             63
  N3                           23                             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"
D80V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(15Q11.2) MUTATED   148  12
  DEL PEAK 41(15Q11.2) WILD-TYPE 365  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(15Q11.2) MUTATED    148   12
  DEL PEAK 41(15Q11.2) WILD-TYPE  365   27
   clus
vv  DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  0                          148                            365
  1                           12                             27
[1] 2 2
[1] FALSE
D80V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(15Q11.2) MUTATED    50 128
  DEL PEAK 41(15Q11.2) WILD-TYPE 132 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(15Q11.2) MUTATED     50  128
  DEL PEAK 41(15Q11.2) WILD-TYPE  132  299
        clus
vv       DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  FEMALE                           50                            132
  MALE                            128                            299
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 41(15Q11.2) MUTATED                                      14
  DEL PEAK 41(15Q11.2) WILD-TYPE                                    57
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(15Q11.2) MUTATED                                                       37
  DEL PEAK 41(15Q11.2) WILD-TYPE                                                    125
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(15Q11.2) MUTATED                                                                  27
  DEL PEAK 41(15Q11.2) WILD-TYPE                                                                54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 41(15Q11.2) MUTATED                                                 29
  DEL PEAK 41(15Q11.2) WILD-TYPE                                               49
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 41(15Q11.2) MUTATED                                                          4
  DEL PEAK 41(15Q11.2) WILD-TYPE                                                       17
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 41(15Q11.2) MUTATED                                                           3
  DEL PEAK 41(15Q11.2) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 41(15Q11.2) MUTATED                                          5
  DEL PEAK 41(15Q11.2) WILD-TYPE                                        8
D80V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 41(15Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 41(15Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(15Q11.2) MUTATED     4 174
  DEL PEAK 41(15Q11.2) WILD-TYPE   2 429
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(15Q11.2) MUTATED      4  174
  DEL PEAK 41(15Q11.2) WILD-TYPE    2  429
     clus
vv    DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          174                            429
[1] 2 2
[1] FALSE
D80V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(15Q11.2) MUTATED    99   6   3   4
  DEL PEAK 41(15Q11.2) WILD-TYPE 248  12  16  21
D80V11, multiclass
    clus
vv   DEL PEAK 41(15Q11.2) MUTATED DEL PEAK 41(15Q11.2) WILD-TYPE
  R0                           99                            248
  R1                            6                             12
  R2                            3                             16
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(15Q11.2) MUTATED      42                         3
  DEL PEAK 41(15Q11.2) WILD-TYPE    87                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 41(15Q11.2) MUTATED                                           0
  DEL PEAK 41(15Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 41(15Q11.2) MUTATED     109
  DEL PEAK 41(15Q11.2) WILD-TYPE   276
D80V13, multiclass
                                           clus
vv                                          DEL PEAK 41(15Q11.2) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              109
                                           clus
vv                                          DEL PEAK 41(15Q11.2) WILD-TYPE
  ASIAN                                                                 87
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                                cls
clus                               0   1
  DEL PEAK 41(15Q11.2) MUTATED     1 115
  DEL PEAK 41(15Q11.2) WILD-TYPE   6 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(15Q11.2) MUTATED      1  115
  DEL PEAK 41(15Q11.2) WILD-TYPE    6  279
                        clus
vv                       DEL PEAK 41(15Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       DEL PEAK 41(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 42(16P13.3) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(16P13.3) MUTATED    96  70
  DEL PEAK 42(16P13.3) WILD-TYPE 258 151
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                           166                            409 
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                            70                            151 
$`DEL PEAK 42(16P13.3) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C 
       32.45         7.69        20.12        42.77        25.41        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH 
       25.22         3.16         8.94        24.00         4.70        32.61 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        1.38         3.16        58.59         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV 
        3.02        12.92        13.48         5.49        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A5 
       46.09        10.36        10.45        12.43         0.10        22.39 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-R6-A6DN 
       12.33         4.47        12.00        12.03         5.16         8.02 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC 
        2.89         1.45        12.69         7.00         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 
        4.80         9.27        19.96        22.82        12.43        42.87 
TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-7197 TCGA-BR-7704 
       15.91         2.10         6.61        18.35         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 
       15.42        28.01         3.45        18.71        12.95         2.66 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-A4CQ 
       16.31        17.52        14.79         0.49        11.54        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        1.48         0.72         1.15        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.07         0.07         0.16         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4441 
        9.34        12.43        11.61        12.20        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-CG-5732 TCGA-D7-5579 
       29.98        19.07        12.03        12.03        69.04        11.93 
TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       20.55        15.22        12.33        11.24        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
        2.96         7.40         7.99        72.23         0.56         5.52 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        12.59        12.10         0.76        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
       11.77         9.67         3.39         5.19         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51         1.81         7.82         2.53         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       37.64         9.86        18.21         6.08         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.67        35.61         5.79        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       13.02        35.24         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91X 
        2.70         1.87        27.35        64.57        36.69         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       52.24         9.04         4.54        64.18        21.04        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       40.08        32.94        17.13        21.11 

$`DEL PEAK 42(16P13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IC-A6RF TCGA-IG-A3I8 
       25.78        31.27        14.30        16.24         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         6.28        30.25         0.30         4.31 
TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        3.68        19.99        21.01        47.93        18.35         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG 
        8.71         2.60        25.12        55.50         2.66        35.97 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       16.47        13.55        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R 
       13.41        83.24         5.92        12.66        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25         0.10        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22        12.33        25.25        10.52        12.23        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13        33.11         7.82         7.59        14.70         7.04 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET 
       20.02        20.38        15.35         4.44        18.81         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        30.71        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.06        11.24         9.17        10.16         3.42         2.66 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       19.73        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        9.44         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        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49        14.43        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55         8.05         0.56         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50        13.08         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53        15.81        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        12.56        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        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-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-5801 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       13.18         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.10        11.31         6.58         0.10        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        8.05         4.01        47.05        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-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-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.36        12.66        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       11.44        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
        0.23        18.08        26.47         1.51        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       19.36        23.84        12.30         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.21         3.45        18.81        18.38         5.36        13.08 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG 
        6.44         5.56        13.51        60.56        20.15         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT 
       19.73        45.67         8.52        61.25         4.60         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87        19.04         0.92 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31         2.50        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        26.24        14.33        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       36.16         7.36         9.73         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72         2.66        11.24        22.09        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       29.98        54.12        26.04        16.14        12.43        10.62 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE 
                         11.69                          13.35 
[1] "0.1 - 72.2 (11.7)"  "0.0 - 122.3 (13.3)"
[1] "hr=" "1.2"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(16P13.3) MUTATED         4        9        9       11        17
  DEL PEAK 42(16P13.3) WILD-TYPE       7       10       39       21        60
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(16P13.3) MUTATED          19        12         35         16
  DEL PEAK 42(16P13.3) WILD-TYPE        65        17         62         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 42(16P13.3) MUTATED            8       13         1
  DEL PEAK 42(16P13.3) WILD-TYPE         40       38         3
D81V3, multiclass
            clus
vv           DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              9                             10
  STAGE IB                              9                             39
  STAGE II                             11                             21
  STAGE IIA                            17                             60
  STAGE IIB                            19                             65
  STAGE III                            12                             17
  STAGE IIIA                           35                             62
  STAGE IIIB                           16                             56
  STAGE IIIC                            8                             40
  STAGE IV                             13                             38
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 42(16P13.3) MUTATED      20  28  88  23
  DEL PEAK 42(16P13.3) WILD-TYPE    33  98 192 101
D81V4, multiclass
       clus
vv      DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  T0+T1                           20                             33
  T2                              28                             98
  T3                              88                            192
  T4                              23                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 42(16P13.3) MUTATED    50  59  30  20
  DEL PEAK 42(16P13.3) WILD-TYPE 150 123  66  77
D81V5, multiclass
    clus
vv   DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  N0                           50                            150
  N1                           59                            123
  N2                           30                             66
  N3                           20                             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"
D81V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(16P13.3) MUTATED   145   8
  DEL PEAK 42(16P13.3) WILD-TYPE 368  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(16P13.3) MUTATED    145    8
  DEL PEAK 42(16P13.3) WILD-TYPE  368   31
   clus
vv  DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  0                          145                            368
  1                            8                             31
[1] 2 2
[1] FALSE
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(16P13.3) MUTATED    41 134
  DEL PEAK 42(16P13.3) WILD-TYPE 141 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(16P13.3) MUTATED     41  134
  DEL PEAK 42(16P13.3) WILD-TYPE  141  293
        clus
vv       DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  FEMALE                           41                            141
  MALE                            134                            293
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 42(16P13.3) MUTATED                                       8
  DEL PEAK 42(16P13.3) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(16P13.3) MUTATED                                                       40
  DEL PEAK 42(16P13.3) WILD-TYPE                                                    122
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(16P13.3) MUTATED                                                                  24
  DEL PEAK 42(16P13.3) WILD-TYPE                                                                57
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 42(16P13.3) MUTATED                                                 26
  DEL PEAK 42(16P13.3) WILD-TYPE                                               52
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 42(16P13.3) MUTATED                                                          8
  DEL PEAK 42(16P13.3) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 42(16P13.3) MUTATED                                                           2
  DEL PEAK 42(16P13.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 42(16P13.3) MUTATED                                          4
  DEL PEAK 42(16P13.3) WILD-TYPE                                        9
D81V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 42(16P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 42(16P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       122
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(16P13.3) MUTATED     2 173
  DEL PEAK 42(16P13.3) WILD-TYPE   4 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(16P13.3) MUTATED      2  173
  DEL PEAK 42(16P13.3) WILD-TYPE    4  430
     clus
vv    DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  NO                             2                              4
  YES                          173                            430
[1] 2 2
[1] FALSE
D81V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(16P13.3) MUTATED    86   5   4   7
  DEL PEAK 42(16P13.3) WILD-TYPE 261  13  15  18
D81V11, multiclass
    clus
vv   DEL PEAK 42(16P13.3) MUTATED DEL PEAK 42(16P13.3) WILD-TYPE
  R0                           86                            261
  R1                            5                             13
  R2                            4                             15
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(16P13.3) MUTATED      36                         6
  DEL PEAK 42(16P13.3) WILD-TYPE    93                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 42(16P13.3) MUTATED                                           0
  DEL PEAK 42(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 42(16P13.3) MUTATED     108
  DEL PEAK 42(16P13.3) WILD-TYPE   277
D81V13, multiclass
                                           clus
vv                                          DEL PEAK 42(16P13.3) MUTATED
  ASIAN                                                               36
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              108
                                           clus
vv                                          DEL PEAK 42(16P13.3) WILD-TYPE
  ASIAN                                                                 93
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                277
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                                cls
clus                               0   1
  DEL PEAK 42(16P13.3) MUTATED     3 102
  DEL PEAK 42(16P13.3) WILD-TYPE   4 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(16P13.3) MUTATED      3  102
  DEL PEAK 42(16P13.3) WILD-TYPE    4  292
                        clus
vv                       DEL PEAK 42(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       DEL PEAK 42(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 43(16P13.3) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(16P13.3) MUTATED    81  56
  DEL PEAK 43(16P13.3) WILD-TYPE 273 165
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                           137                            438 
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                            56                            165 
$`DEL PEAK 43(16P13.3) MUTATED`
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93E 
       32.45        20.12        42.77        25.41        23.18        25.22 
TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OS 
        3.16        24.00         4.70        32.61         3.16        58.59 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI 
        0.36         7.40         3.95         3.02        12.92        13.48 
TCGA-L5-A8NN TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
        5.49        27.12        52.57        10.36        10.45        12.43 
TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A7HY TCGA-Q9-A6FU 
        0.10        22.39        12.33        12.00        12.03         5.16 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        8.02         5.06         6.35         9.30        15.78         1.45 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP 
       12.69         7.00         5.29         4.80         9.27        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-4183 
       22.82        12.43        42.87        15.91         2.10         6.61 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 
        9.21        35.24        15.42        28.01         3.45        18.71 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 
       12.95         2.66        16.31        17.52        14.79         0.49 
TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF 
       11.54         7.53        22.26         1.48         0.72         1.15 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 
        0.07         0.07         0.07         0.07         0.16         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4444 
        3.42         9.34        12.43        11.61        12.20        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6822 
       19.07        12.03        12.03        11.93        15.22        12.33 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8211 
       11.31         2.96         7.40         7.99        72.23        13.58 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        12.59        12.10         0.76        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
       11.77        23.84        12.30         9.67        27.42         3.39 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 
        6.74        12.59         5.56        37.64         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       11.05        16.67        35.61         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       13.25        13.02        18.48        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91Z TCGA-VQ-A922 
       17.85         1.87        27.35        64.57        52.24         9.04 
TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       21.04        40.08        32.94        17.13        21.11 

$`DEL PEAK 43(16P13.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        31.27        14.30        16.24         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 
       33.27        20.09         0.85        20.78         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        3.88         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
      122.10        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H 
       21.70        31.56        24.03         6.28        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM 
        4.31         8.94         3.68        19.99        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         3.32         7.17         1.38         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        7.13         7.43         6.94         8.71         2.60        25.12 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        35.97        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        7.76        21.37         8.71        13.41        83.24        46.09 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
        5.92        12.66        13.41         0.10        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25         0.10        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59         0.10        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO 
       12.33        25.25        10.52        12.23        13.18         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         7.59        14.70         7.04        29.59 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       53.95         2.89        20.02        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        4.44        18.81         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       10.16         3.42         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       32.94        12.82        24.76        23.93        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73        12.43         9.07        12.76        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.56         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       14.04         3.32        11.80        19.17         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56        13.87         6.08        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.10        11.31         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        21.99         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85        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-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
       15.65         8.38         4.34         7.13         0.62        16.24 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
        0.23        18.08        26.47         1.51        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
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-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-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       60.56        20.15         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21         8.52        61.25         4.60         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E2 
       57.44         8.94        16.87        19.04         0.92        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31        22.19         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        26.24        14.33        65.16        36.69 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        11.93        61.22        18.74        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        64.18         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       42.54        11.24        22.09        18.41        28.41        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        12.43        10.62         0.79 

  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE 
                        12.030                         13.165 
[1] "0.1 - 72.2 (12.0)"  "0.0 - 122.3 (13.2)"
[1] "hr=" "1.2"
D82V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(16P13.3) MUTATED         4        6        8        9        15
  DEL PEAK 43(16P13.3) WILD-TYPE       7       13       40       23        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(16P13.3) MUTATED          19        12         31         11
  DEL PEAK 43(16P13.3) WILD-TYPE        65        17         66         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 43(16P13.3) MUTATED            7        8         1
  DEL PEAK 43(16P13.3) WILD-TYPE         41       43         3
D82V3, multiclass
            clus
vv           DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              6                             13
  STAGE IB                              8                             40
  STAGE II                              9                             23
  STAGE IIA                            15                             62
  STAGE IIB                            19                             65
  STAGE III                            12                             17
  STAGE IIIA                           31                             66
  STAGE IIIB                           11                             61
  STAGE IIIC                            7                             41
  STAGE IV                              8                             43
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 43(16P13.3) MUTATED      16  23  74  22
  DEL PEAK 43(16P13.3) WILD-TYPE    37 103 206 102
D82V4, multiclass
       clus
vv      DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  T0+T1                           16                             37
  T2                              23                            103
  T3                              74                            206
  T4                              22                            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 43(16P13.3) MUTATED    43  55  20  16
  DEL PEAK 43(16P13.3) WILD-TYPE 157 127  76  81
D82V5, multiclass
    clus
vv   DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  N0                           43                            157
  N1                           55                            127
  N2                           20                             76
  N3                           16                             81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(16P13.3) MUTATED   125   6
  DEL PEAK 43(16P13.3) WILD-TYPE 388  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(16P13.3) MUTATED    125    6
  DEL PEAK 43(16P13.3) WILD-TYPE  388   33
   clus
vv  DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  0                          125                            388
  1                            6                             33
[1] 2 2
[1] FALSE
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(16P13.3) MUTATED    36 110
  DEL PEAK 43(16P13.3) WILD-TYPE 146 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(16P13.3) MUTATED     36  110
  DEL PEAK 43(16P13.3) WILD-TYPE  146  317
        clus
vv       DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  FEMALE                           36                            146
  MALE                            110                            317
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 43(16P13.3) MUTATED                                       8
  DEL PEAK 43(16P13.3) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(16P13.3) MUTATED                                                       31
  DEL PEAK 43(16P13.3) WILD-TYPE                                                    131
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(16P13.3) MUTATED                                                                  17
  DEL PEAK 43(16P13.3) WILD-TYPE                                                                64
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 43(16P13.3) MUTATED                                                 24
  DEL PEAK 43(16P13.3) WILD-TYPE                                               54
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 43(16P13.3) MUTATED                                                          7
  DEL PEAK 43(16P13.3) WILD-TYPE                                                       14
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 43(16P13.3) MUTATED                                                           2
  DEL PEAK 43(16P13.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 43(16P13.3) MUTATED                                          3
  DEL PEAK 43(16P13.3) WILD-TYPE                                       10
D82V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 43(16P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 43(16P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(16P13.3) MUTATED     2 144
  DEL PEAK 43(16P13.3) WILD-TYPE   4 459
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(16P13.3) MUTATED      2  144
  DEL PEAK 43(16P13.3) WILD-TYPE    4  459
     clus
vv    DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  NO                             2                              4
  YES                          144                            459
[1] 2 2
[1] FALSE
D82V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(16P13.3) MUTATED    70   5   3   6
  DEL PEAK 43(16P13.3) WILD-TYPE 277  13  16  19
D82V11, multiclass
    clus
vv   DEL PEAK 43(16P13.3) MUTATED DEL PEAK 43(16P13.3) WILD-TYPE
  R0                           70                            277
  R1                            5                             13
  R2                            3                             16
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(16P13.3) MUTATED      35                         6
  DEL PEAK 43(16P13.3) WILD-TYPE    94                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 43(16P13.3) MUTATED                                           0
  DEL PEAK 43(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 43(16P13.3) MUTATED      84
  DEL PEAK 43(16P13.3) WILD-TYPE   301
D82V13, multiclass
                                           clus
vv                                          DEL PEAK 43(16P13.3) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               84
                                           clus
vv                                          DEL PEAK 43(16P13.3) WILD-TYPE
  ASIAN                                                                 94
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(16P13.3) MUTATED     3  85
  DEL PEAK 43(16P13.3) WILD-TYPE   4 309
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(16P13.3) MUTATED      3   85
  DEL PEAK 43(16P13.3) WILD-TYPE    4  309
                        clus
vv                       DEL PEAK 43(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 43(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            309
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 44(16Q23.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(16Q23.1) MUTATED   153  93
  DEL PEAK 44(16Q23.1) WILD-TYPE 201 128
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                           246                            329 
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                            93                            128 
$`DEL PEAK 44(16Q23.1) MUTATED`
TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A97H 
        4.21        20.09        20.12         3.88         0.53        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D 
      122.10        60.39        42.77        25.41        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       25.22         3.16         8.94        24.00         3.68        21.01 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       18.35         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43         2.60         0.36         3.95         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        35.97        16.47        13.22         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4MQ 
       10.45        13.41         0.10        13.25        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN 
       13.22        10.52        12.00        12.03        13.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59         5.06        14.70         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       15.78         2.89         1.45        12.69         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-Z6-A8JD 
        4.80         9.27        18.81        19.96        22.82         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4279 TCGA-BR-6456 
        9.44         6.61         6.97        18.35         9.57        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       19.33        26.10        18.05        24.76        35.24        15.42 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       18.15        28.73         3.45        18.71        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8361 
        9.60         0.56        12.95         2.66        16.31        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8484 
       13.08         0.26        17.52        19.17        14.79        25.18 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A452 
        0.49        11.54        16.44         8.22        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       22.26         0.72        20.65        20.42         1.15        13.64 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 
       13.15         0.30         0.07         0.07         0.07         0.16 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4305 
        0.13         3.42        12.43        11.61        12.20        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        7.99         8.05        54.08        47.05        19.07        12.03 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        7.07        22.98        30.97       105.07        12.03        15.02 
TCGA-CG-5727 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6526 
       79.07        12.36        12.66        11.93        13.35        17.19 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT 
       15.22        12.79        10.55        19.50        18.21        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       15.16        13.78        11.24        11.31         2.96        15.65 
TCGA-D7-A747 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF 
        8.38        16.24        72.23        14.07        22.29         5.52 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 
       18.08         1.51         5.92        12.59        12.10         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        5.59        12.30        22.75        11.77         8.98         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       10.19         0.26         2.10        23.84        12.30         9.67 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP 
       27.42         3.45        18.81        18.38        13.08         6.44 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         1.81         7.82        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
       20.15        37.64         9.86         6.08         9.24        11.05 
TCGA-RD-A7C1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       16.67         8.94        35.61         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.46        13.02         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
       17.85         1.87        23.41        64.57        14.33        36.69 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       11.93        61.22        22.68         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-A94U 
       52.24         9.04         4.54         5.72        42.54        22.09 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       40.08        32.94        17.13        54.12        26.04         0.79 

$`DEL PEAK 44(16Q23.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
       25.78        14.30        58.55        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT 
       33.27         0.85        20.78         2.63        18.64         9.30 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       17.03         0.79        23.41        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       21.70        24.03         6.28        30.25         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
        4.70        32.61        19.99        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH 
        1.38         6.94         8.71        25.12         7.40        12.92 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
       13.48        13.55        21.37        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.43         0.10        13.15        15.35         0.10        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39         0.10        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO 
       11.54         4.47        12.33        25.25        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BV 
       33.11         5.16         7.82         7.04        29.59        20.02 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35         4.44        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        30.71        18.18        42.87 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        15.06        11.24         9.17        15.91        10.16 
TCGA-Z6-A8JE TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        2.10         9.47         4.64         7.43        30.90         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        25.61        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       23.93        28.01        15.32        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 
       17.49        14.43        12.26        20.55         8.05         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       15.58         7.40         6.18        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8382 
        4.31        14.04         3.32        11.80         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       15.81         9.34        13.45         6.28         7.53        15.81 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS 
        9.86        15.68        10.68        12.56         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        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-5799 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8527 
        5.13         2.83         3.25        13.18         0.07         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-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        9.34        11.31         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        3.02        27.02         1.02         4.01        14.01        29.98 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 
       21.99         0.00         9.01        18.97        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5726 
       36.00         1.02         0.99         6.02         0.99        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6518 
       65.10         4.01        69.04        21.07         7.99        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       20.55        18.84        18.54        18.61        17.85        10.26 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       15.98        11.31        12.33        24.72        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4Z0 
       14.66        21.14        20.91        16.44         5.92        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       13.71        11.44         9.76         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        0.23        26.47        14.27        14.17        11.41        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ 
       24.30        11.84        24.20         3.25        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 
       29.98         0.10         6.51        12.95        19.36         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
        8.81        21.21         3.39         5.36         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ 
        6.74        12.59         5.56         2.53         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT 
       45.67        18.21         8.52        61.25         4.60         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8E0 
       71.38        57.44        16.87        19.04        13.25        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       34.29        16.31         2.50         2.70         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91N 
       13.35        26.24        27.35        65.16        11.70        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       20.81        36.16         7.36         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
       64.18        21.04         2.66        11.24        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       29.98        16.14        21.11        12.43        10.62 

  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                         122.1                          122.3 
  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE 
                        12.625                         12.820 
[1] "0.1 - 122.1 (12.6)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1"  
D83V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(16Q23.1) MUTATED         5        8       18       17        27
  DEL PEAK 44(16Q23.1) WILD-TYPE       6       11       30       15        50
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(16Q23.1) MUTATED          39        16         45         22
  DEL PEAK 44(16Q23.1) WILD-TYPE        45        13         52         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 44(16Q23.1) MUTATED           25       14         3
  DEL PEAK 44(16Q23.1) WILD-TYPE         23       37         1
D83V3, multiclass
            clus
vv           DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              8                             11
  STAGE IB                             18                             30
  STAGE II                             17                             15
  STAGE IIA                            27                             50
  STAGE IIB                            39                             45
  STAGE III                            16                             13
  STAGE IIIA                           45                             52
  STAGE IIIB                           22                             50
  STAGE IIIC                           25                             23
  STAGE IV                             14                             37
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 44(16Q23.1) MUTATED      24  53 122  46
  DEL PEAK 44(16Q23.1) WILD-TYPE    29  73 158  78
D83V4, multiclass
       clus
vv      DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  T0+T1                           24                             29
  T2                              53                             73
  T3                             122                            158
  T4                              46                             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 44(16Q23.1) MUTATED    76  85  35  44
  DEL PEAK 44(16Q23.1) WILD-TYPE 124  97  61  53
D83V5, multiclass
    clus
vv   DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  N0                           76                            124
  N1                           85                             97
  N2                           35                             61
  N3                           44                             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"
D83V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(16Q23.1) MUTATED   222   9
  DEL PEAK 44(16Q23.1) WILD-TYPE 291  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(16Q23.1) MUTATED    222    9
  DEL PEAK 44(16Q23.1) WILD-TYPE  291   30
   clus
vv  DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  0                          222                            291
  1                            9                             30
[1] 2 2
[1] FALSE
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(16Q23.1) MUTATED    68 191
  DEL PEAK 44(16Q23.1) WILD-TYPE 114 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(16Q23.1) MUTATED     68  191
  DEL PEAK 44(16Q23.1) WILD-TYPE  114  236
        clus
vv       DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  FEMALE                           68                            114
  MALE                            191                            236
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 44(16Q23.1) MUTATED                                      23
  DEL PEAK 44(16Q23.1) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(16Q23.1) MUTATED                                                       63
  DEL PEAK 44(16Q23.1) WILD-TYPE                                                     99
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(16Q23.1) MUTATED                                                                  31
  DEL PEAK 44(16Q23.1) WILD-TYPE                                                                50
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 44(16Q23.1) MUTATED                                                 38
  DEL PEAK 44(16Q23.1) WILD-TYPE                                               40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 44(16Q23.1) MUTATED                                                         11
  DEL PEAK 44(16Q23.1) WILD-TYPE                                                       10
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 44(16Q23.1) MUTATED                                                           6
  DEL PEAK 44(16Q23.1) WILD-TYPE                                                         2
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 44(16Q23.1) MUTATED                                          6
  DEL PEAK 44(16Q23.1) WILD-TYPE                                        7
D83V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 44(16Q23.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           31
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     6
                                                                   clus
vv                                                                  DEL PEAK 44(16Q23.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(16Q23.1) MUTATED     5 254
  DEL PEAK 44(16Q23.1) WILD-TYPE   1 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(16Q23.1) MUTATED      5  254
  DEL PEAK 44(16Q23.1) WILD-TYPE    1  349
     clus
vv    DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  NO                             5                              1
  YES                          254                            349
[1] 2 2
[1] FALSE
D83V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(16Q23.1) MUTATED   144   9   4   9
  DEL PEAK 44(16Q23.1) WILD-TYPE 203   9  15  16
D83V11, multiclass
    clus
vv   DEL PEAK 44(16Q23.1) MUTATED DEL PEAK 44(16Q23.1) WILD-TYPE
  R0                          144                            203
  R1                            9                              9
  R2                            4                             15
  RX                            9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(16Q23.1) MUTATED      51                         4
  DEL PEAK 44(16Q23.1) WILD-TYPE    78                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(16Q23.1) MUTATED                                           0
  DEL PEAK 44(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 44(16Q23.1) MUTATED     166
  DEL PEAK 44(16Q23.1) WILD-TYPE   219
D83V13, multiclass
                                           clus
vv                                          DEL PEAK 44(16Q23.1) MUTATED
  ASIAN                                                               51
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              166
                                           clus
vv                                          DEL PEAK 44(16Q23.1) WILD-TYPE
  ASIAN                                                                 78
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V14, binary
                                cls
clus                               0   1
  DEL PEAK 44(16Q23.1) MUTATED     4 154
  DEL PEAK 44(16Q23.1) WILD-TYPE   3 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(16Q23.1) MUTATED      4  154
  DEL PEAK 44(16Q23.1) WILD-TYPE    3  240
                        clus
vv                       DEL PEAK 44(16Q23.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          154
                        clus
vv                       DEL PEAK 44(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            240
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 45(17P12) MUTATION ANALYSIS
D84V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 45(17P12) MUTATED   148 102
  DEL PEAK 45(17P12) WILD-TYPE 206 119
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                         250                          325 
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                         102                          119 
$`DEL PEAK 45(17P12) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       25.78         7.63         5.92        13.94         8.94         4.21 
TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       32.45        18.64         3.88         0.79        23.41        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-JY-A93E 
      122.10        60.39        42.77        25.41        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO 
       30.25        24.00         3.68         4.70        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        7.17         4.90        29.00         7.13         7.43         2.60 
TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NJ 
        0.36         3.95        55.50        35.97        13.48        16.47 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.22         5.49         8.71        13.41        27.12        83.24 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
        5.92        10.45        12.66        13.15        15.35        13.25 
TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.59        12.33        10.52        13.18        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 
        7.82         7.59         5.06         7.04        29.59         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
       15.78         1.45        12.69         7.00        20.02        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        4.80         9.27         4.44        19.96        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55        18.31         8.12        18.18        46.19        11.24 
TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN 
       10.16         2.66        19.73        11.70        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 
        6.61         6.18        17.29        19.33         9.17        12.16 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 
        9.21        35.24        15.42        28.73        18.71        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.69         9.60        12.95         2.66        16.31        15.58 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 
       19.50        13.08        14.04        14.79         5.39        25.18 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       11.54        16.44         9.86        10.68        13.87         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       22.26         1.48         0.72        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
        1.15         3.25        13.15         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.13         0.13         0.13         3.42        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        12.20        20.02         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 
       19.07         7.07        30.97        36.00         1.02        15.02 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       79.07         4.01        69.04        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       11.31        12.33        14.66        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 
        7.40         7.99        16.24        72.23        11.38        14.07 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 
       17.06        13.58         0.56         0.23        26.47         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       12.59        14.17        12.10        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 
        6.25         2.10        12.95        12.30        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39        18.38         5.19         1.41         6.44 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       12.59         1.81         7.82         2.53         5.56        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 
        9.86        45.67        18.21         9.24         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       18.48        35.24         7.73        46.26        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       17.85         1.87        13.35        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       65.16        18.74        20.81        36.16         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U 
       52.24         9.04         4.54        64.18        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        40.08        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        21.11        12.43         0.79 

$`DEL PEAK 45(17P12) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF 
       31.27        14.30        58.55        16.24         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16        44.75        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        23.18        24.03         6.28         3.16         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        4.31         8.94        19.99        21.01        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W 
        1.38         3.16        58.59         6.94         8.71        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        7.40         3.02         2.66        12.92        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O 
       21.37        52.57        46.09        10.36        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
        0.10         0.10         0.10        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        25.25        12.00        12.23        12.03 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
        0.13         8.02        14.70         6.35        53.95         2.89 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY 
        5.29         3.42        15.35        18.81        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       42.87        15.06         9.17        15.91         3.42         2.10 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.87        13.68        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       32.94        12.82        24.76        23.93        28.01        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       14.43        12.26        20.55         8.05         0.56         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        7.40         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       15.81        15.68         8.22        12.56         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        19.36         0.46        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8530 
        2.83        13.18         0.30         0.07         0.07         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
        0.10         0.10         0.10         9.34         6.58         0.10 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4460 
       12.62        15.95         1.02        14.01        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        0.00         9.01        18.97        12.00        22.98         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       65.10        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 
       18.61        17.85        12.79        10.55        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
        0.62        14.47        21.27         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 
       59.54         5.03         5.52        18.08         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.51        10.19         0.26        19.36        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN 
        9.67         8.88         8.81         3.45         5.36        13.08 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93G 
        6.74         6.51         5.56        13.51        60.56        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73         8.52        61.25         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31        22.19         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        26.24        36.69        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       22.68         1.71         7.36         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A 
        5.72        21.04         2.66        42.54        28.41        32.94 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                       122.1                        122.3 
  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE 
                       12.74                        12.76 
[1] "0.1 - 122.1 (12.7)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D84V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(17P12) MUTATED         6        8       21       15        30
  DEL PEAK 45(17P12) WILD-TYPE       5       11       27       17        47
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(17P12) MUTATED          35        15         40         33
  DEL PEAK 45(17P12) WILD-TYPE        49        14         57         39
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 45(17P12) MUTATED           18       21         1
  DEL PEAK 45(17P12) WILD-TYPE         30       30         3
D84V3, multiclass
            clus
vv           DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  STAGE I                             6                            5
  STAGE IA                            8                           11
  STAGE IB                           21                           27
  STAGE II                           15                           17
  STAGE IIA                          30                           47
  STAGE IIB                          35                           49
  STAGE III                          15                           14
  STAGE IIIA                         40                           57
  STAGE IIIB                         33                           39
  STAGE IIIC                         18                           30
  STAGE IV                           21                           30
  STAGE IVA                           1                            3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  DEL PEAK 45(17P12) MUTATED      22  56 126  43
  DEL PEAK 45(17P12) WILD-TYPE    31  70 154  81
D84V4, multiclass
       clus
vv      DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  T0+T1                         22                           31
  T2                            56                           70
  T3                           126                          154
  T4                            43                           81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 45(17P12) MUTATED    82  77  46  39
  DEL PEAK 45(17P12) WILD-TYPE 118 105  50  58
D84V5, multiclass
    clus
vv   DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  N0                         82                          118
  N1                         77                          105
  N2                         46                           50
  N3                         39                           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"
D84V6, binary
                              cls
clus                             0   1
  DEL PEAK 45(17P12) MUTATED   216  13
  DEL PEAK 45(17P12) WILD-TYPE 297  26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(17P12) MUTATED    216   13
  DEL PEAK 45(17P12) WILD-TYPE  297   26
   clus
vv  DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  0                        216                          297
  1                         13                           26
[1] 2 2
[1] FALSE
D84V7, binary
                              cls
clus                             0   1
  DEL PEAK 45(17P12) MUTATED    65 193
  DEL PEAK 45(17P12) WILD-TYPE 117 234
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(17P12) MUTATED     65  193
  DEL PEAK 45(17P12) WILD-TYPE  117  234
        clus
vv       DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  FEMALE                         65                          117
  MALE                          193                          234
[1] 2 2
[1] FALSE
                              vv
clus                           STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 45(17P12) MUTATED                                      15
  DEL PEAK 45(17P12) WILD-TYPE                                    56
                              vv
clus                           STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(17P12) MUTATED                                                       58
  DEL PEAK 45(17P12) WILD-TYPE                                                    104
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(17P12) MUTATED                                                                  42
  DEL PEAK 45(17P12) WILD-TYPE                                                                39
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 45(17P12) MUTATED                                                 41
  DEL PEAK 45(17P12) WILD-TYPE                                               37
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 45(17P12) MUTATED                                                          9
  DEL PEAK 45(17P12) WILD-TYPE                                                       12
                              vv
clus                           STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 45(17P12) MUTATED                                                           4
  DEL PEAK 45(17P12) WILD-TYPE                                                         4
                              vv
clus                           STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 45(17P12) MUTATED                                          8
  DEL PEAK 45(17P12) WILD-TYPE                                        5
D84V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 45(17P12) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                     15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                    58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                          41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                   9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                  4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                   8
                                                                   clus
vv                                                                  DEL PEAK 45(17P12) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V9, binary
                              cls
clus                             0   1
  DEL PEAK 45(17P12) MUTATED     4 254
  DEL PEAK 45(17P12) WILD-TYPE   2 349
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(17P12) MUTATED      4  254
  DEL PEAK 45(17P12) WILD-TYPE    2  349
     clus
vv    DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  NO                           4                            2
  YES                        254                          349
[1] 2 2
[1] FALSE
D84V10, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 45(17P12) MUTATED   142   9   8   5
  DEL PEAK 45(17P12) WILD-TYPE 205   9  11  20
D84V11, multiclass
    clus
vv   DEL PEAK 45(17P12) MUTATED DEL PEAK 45(17P12) WILD-TYPE
  R0                        142                          205
  R1                          9                            9
  R2                          8                           11
  RX                          5                           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(17P12) MUTATED      47                         4
  DEL PEAK 45(17P12) WILD-TYPE    82                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 45(17P12) MUTATED                                           1   164
  DEL PEAK 45(17P12) WILD-TYPE                                         0   221
D84V13, multiclass
                                           clus
vv                                          DEL PEAK 45(17P12) MUTATED
  ASIAN                                                             47
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            164
                                           clus
vv                                          DEL PEAK 45(17P12) WILD-TYPE
  ASIAN                                                               82
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V14, binary
                              cls
clus                             0   1
  DEL PEAK 45(17P12) MUTATED     3 146
  DEL PEAK 45(17P12) WILD-TYPE   4 248
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(17P12) MUTATED      3  146
  DEL PEAK 45(17P12) WILD-TYPE    4  248
                        clus
vv                       DEL PEAK 45(17P12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        146
                        clus
vv                       DEL PEAK 45(17P12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          248
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 46(17Q24.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(17Q24.3) MUTATED    59  36
  DEL PEAK 46(17Q24.3) WILD-TYPE 295 185
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                            95                            480 
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                            36                            185 
$`DEL PEAK 46(17Q24.3) MUTATED`
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FD TCGA-JY-A938 
        8.94         4.21        23.41        14.50        68.02        25.41 
TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NG 
       32.61         3.16         0.36         7.40         3.95        35.97 
TCGA-L5-A8NR TCGA-LN-A49L TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
        8.71        10.45        10.52        12.00        12.03        13.18 
TCGA-Q9-A6FU TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-A8Q7 
        5.16        15.35         4.44        22.82        28.11        42.87 
TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-A5TJ TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 
       10.16         2.66        11.01        19.33         9.17        35.24 
TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8373 
       15.42        18.71         0.69        16.31        19.50        14.79 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4J1 
        3.72         9.21         9.86        13.87         7.53         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 
       13.51        20.65         1.15        13.64         0.07         0.10 
TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
        0.13        11.31        11.61        12.20        20.02        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 
        4.01        14.01        47.05         7.07         4.01        11.93 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A 
       17.19        15.22        14.66        16.44        11.31         7.40 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GP 
       16.24         0.23         5.92        12.59        14.17         8.98 
TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 
       12.95        18.81         3.39        37.64         9.86        45.67 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.61        16.67       115.69         8.94         5.79         5.46 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y 
       46.26        12.79        64.57        18.74         9.50         9.73 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94U TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        4.54         5.72        22.09        16.14         0.79 

$`DEL PEAK 46(17Q24.3) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
       13.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 
        3.88         9.30         0.53        17.03         0.79        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86         4.67        12.16       122.10        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       60.39         3.68        41.52        42.77        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
        0.30         4.31         8.94        24.00         3.68         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       19.99        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        1.38        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE 
        6.94         8.71         2.60        25.12         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
        7.76         5.49        21.37        13.41        27.12        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        46.09        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       13.41         0.10        13.15        15.35         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 
        4.47        12.33        25.25        12.23         0.13        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        7.82         8.02         7.59         5.06        14.70         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       29.59         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB 
        1.45        12.69         7.00        20.02        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        3.42         4.80         9.27        18.81        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
        1.55        18.31         8.12        30.71        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.06        11.24         9.17        15.91         3.42         2.10 
TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       19.73        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       17.29        13.68        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        32.94        12.82         9.21        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
        9.07        12.76        17.49        14.43        11.44        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
        3.32        11.80        19.17         0.26        15.85         5.39 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         6.28         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       16.44        15.68         8.22        10.68        12.56         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-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-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        3.42         9.34        12.43         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        19.07        12.03        21.99         0.00         9.01 
TCGA-CG-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        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        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        18.21        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44         9.76         2.96        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13         0.62         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         5.52        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-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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        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        23.84        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       27.42        21.21         3.45        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.08         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        20.15         3.72        19.73        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       61.25         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       35.61        16.87        19.04         0.92        48.79        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       32.48         7.73        28.96        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        26.24        27.35        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        36.16         7.36        52.24         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       17.13        54.12        26.04        21.11        12.43        10.62 

  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE 
                         12.00                          12.82 
[1] "0.1 - 115.7 (12.0)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(17Q24.3) MUTATED         1        2        2        3        15
  DEL PEAK 46(17Q24.3) WILD-TYPE      10       17       46       29        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(17Q24.3) MUTATED          13         6         19         15
  DEL PEAK 46(17Q24.3) WILD-TYPE        71        23         78         57
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 46(17Q24.3) MUTATED            7        9         1
  DEL PEAK 46(17Q24.3) WILD-TYPE         41       42         3
D85V3, multiclass
            clus
vv           DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              2                             17
  STAGE IB                              2                             46
  STAGE II                              3                             29
  STAGE IIA                            15                             62
  STAGE IIB                            13                             71
  STAGE III                             6                             23
  STAGE IIIA                           19                             78
  STAGE IIIB                           15                             57
  STAGE IIIC                            7                             41
  STAGE IV                              9                             42
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 46(17Q24.3) MUTATED       7  14  52  24
  DEL PEAK 46(17Q24.3) WILD-TYPE    46 112 228 100
D85V4, multiclass
       clus
vv      DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  T0+T1                            7                             46
  T2                              14                            112
  T3                              52                            228
  T4                              24                            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 46(17Q24.3) MUTATED    29  27  22  17
  DEL PEAK 46(17Q24.3) WILD-TYPE 171 155  74  80
D85V5, multiclass
    clus
vv   DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  N0                           29                            171
  N1                           27                            155
  N2                           22                             74
  N3                           17                             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"
D85V6, binary
                                cls
clus                               0   1
  DEL PEAK 46(17Q24.3) MUTATED    89   5
  DEL PEAK 46(17Q24.3) WILD-TYPE 424  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(17Q24.3) MUTATED     89    5
  DEL PEAK 46(17Q24.3) WILD-TYPE  424   34
   clus
vv  DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  0                           89                            424
  1                            5                             34
[1] 2 2
[1] FALSE
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(17Q24.3) MUTATED    34  68
  DEL PEAK 46(17Q24.3) WILD-TYPE 148 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(17Q24.3) MUTATED     34   68
  DEL PEAK 46(17Q24.3) WILD-TYPE  148  359
        clus
vv       DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  FEMALE                           34                            148
  MALE                             68                            359
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 46(17Q24.3) MUTATED                                       7
  DEL PEAK 46(17Q24.3) WILD-TYPE                                    64
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(17Q24.3) MUTATED                                                       27
  DEL PEAK 46(17Q24.3) WILD-TYPE                                                    135
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(17Q24.3) MUTATED                                                                  15
  DEL PEAK 46(17Q24.3) WILD-TYPE                                                                66
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 46(17Q24.3) MUTATED                                                 19
  DEL PEAK 46(17Q24.3) WILD-TYPE                                               59
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 46(17Q24.3) MUTATED                                                          3
  DEL PEAK 46(17Q24.3) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 46(17Q24.3) MUTATED                                                           2
  DEL PEAK 46(17Q24.3) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 46(17Q24.3) MUTATED                                          3
  DEL PEAK 46(17Q24.3) WILD-TYPE                                       10
D85V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 46(17Q24.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     3
                                                                   clus
vv                                                                  DEL PEAK 46(17Q24.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V9, binary
                                cls
clus                               0   1
  DEL PEAK 46(17Q24.3) MUTATED     0 102
  DEL PEAK 46(17Q24.3) WILD-TYPE   6 501
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(17Q24.3) MUTATED      0  102
  DEL PEAK 46(17Q24.3) WILD-TYPE    6  501
     clus
vv    DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  NO                             0                              6
  YES                          102                            501
[1] 2 2
[1] FALSE
D85V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(17Q24.3) MUTATED    55   4   6   6
  DEL PEAK 46(17Q24.3) WILD-TYPE 292  14  13  19
D85V11, multiclass
    clus
vv   DEL PEAK 46(17Q24.3) MUTATED DEL PEAK 46(17Q24.3) WILD-TYPE
  R0                           55                            292
  R1                            4                             14
  R2                            6                             13
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(17Q24.3) MUTATED      22                         1
  DEL PEAK 46(17Q24.3) WILD-TYPE   107                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 46(17Q24.3) MUTATED                                           1
  DEL PEAK 46(17Q24.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 46(17Q24.3) MUTATED      64
  DEL PEAK 46(17Q24.3) WILD-TYPE   321
D85V13, multiclass
                                           clus
vv                                          DEL PEAK 46(17Q24.3) MUTATED
  ASIAN                                                               22
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               64
                                           clus
vv                                          DEL PEAK 46(17Q24.3) WILD-TYPE
  ASIAN                                                                107
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V14, binary
                                cls
clus                               0   1
  DEL PEAK 46(17Q24.3) MUTATED     1  67
  DEL PEAK 46(17Q24.3) WILD-TYPE   6 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(17Q24.3) MUTATED      1   67
  DEL PEAK 46(17Q24.3) WILD-TYPE    6  327
                        clus
vv                       DEL PEAK 46(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 46(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            327
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 47(18Q12.2) MUTATION ANALYSIS
D86V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(18Q12.2) MUTATED   164 106
  DEL PEAK 47(18Q12.2) WILD-TYPE 190 115
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                           270                            305 
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                           106                            115 
$`DEL PEAK 47(18Q12.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        31.27        58.55         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
       32.45         7.69         0.85         2.63         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        0.79        23.41         9.96        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        42.77        25.41        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
       24.03         3.16         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT 
        4.70        32.61         3.32         7.17         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
       29.00         7.13         7.43         6.94         2.60         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI 
        3.02        55.50         2.66        35.97        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22        21.37         8.71        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       27.12        83.24        52.57        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 
       12.43        13.41         0.10        15.35        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX 
       22.39         0.10        12.33        13.22         4.47        12.23 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        33.11         5.16         7.82         8.02         7.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.02         5.29         3.42         9.27        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43        18.31         8.12        18.18        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 
        6.18         9.57        17.29        13.68        26.10        12.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       35.24        15.42        15.32        28.73         3.45         9.07 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
       11.44        12.95        16.31        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-8686 
        3.32        20.22        15.81         0.49         9.86        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY 
        8.22        10.68        13.87         7.53        22.26        12.89 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        0.66        13.51        13.64         3.25        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         0.13         3.42        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       12.20        20.02         3.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        47.05        19.07        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       22.98        30.97         1.02        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.36        19.13        20.55        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       10.26        15.98        12.33        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
       21.14        14.27        16.44        15.16        11.24         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C 
        2.96        15.65         7.40         0.62         7.99        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       19.53        14.07        22.29        17.06        13.58         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        5.52         5.92        14.17        12.10        10.62        24.30 
TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       12.30        22.75        11.77         8.98         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.95        23.84         9.67         3.45        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        1.41         6.74         5.56         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        60.56        20.15        37.64        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        8.52         6.08         9.24        16.67        37.91       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK 
       18.48        35.24         7.73        22.19         2.50        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       13.35        27.35        36.16         9.50        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U 
        2.01         4.54        64.18        42.54        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       18.41        32.94        29.98        26.04        12.43         0.79 

$`DEL PEAK 47(18Q12.2) WILD-TYPE`
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IC-A6RF TCGA-IG-A3I8 
       14.30         7.63         5.92        13.94         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.09        20.78        20.12        18.64         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB 
       12.82        14.86         4.67       122.10        44.75        60.39 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI 
       41.52        21.70         6.28        30.25         4.31        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88T 
       21.01        47.93        18.35         1.38        58.59         8.71 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
       25.12         0.36         7.40         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
        5.92        13.15         0.10         0.10        12.46        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.76        12.59        15.52        11.54        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       10.52        12.00        12.03         0.13         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RE 
        7.04        29.59         9.30        15.78        20.38         4.80 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       15.35         4.44        18.81         1.55        28.11        30.71 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 
       42.87        11.24         2.10        26.70         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        18.35        30.90         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.87        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       32.94        12.82         9.21        24.76        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       18.15        12.43        12.76        18.71        17.49        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 
       13.08         0.26        17.52        26.33         4.31        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.18         9.21         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T 
        6.28         7.53        11.54        15.81        16.44        12.56 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08         1.48        13.41        13.51         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
       14.17         0.53        12.82        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.42         1.15        11.57         5.13         2.83        13.15 
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         9.34        11.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        6.58         0.10        12.62        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        12.03        21.99         0.00         9.01 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        79.07        65.10        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
       12.66        11.93        18.84        18.61        17.85        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       12.79        10.55        11.31        24.72        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       20.91         5.92        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       11.44         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX 
       72.23        21.27         3.48        59.54         5.03         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        12.59        11.41 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        0.76         5.59        11.84        24.20         3.25        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        10.19         0.26 
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-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81         3.39         5.36        13.08         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI 
        6.51         7.82         3.72        19.73         9.86        61.25 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        4.60        11.05         8.61         5.13       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        21.73        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       34.29        46.26        16.31        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 
       20.81        22.68         1.71         7.36         9.73        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 
        6.58         5.72        21.04         2.66        40.08        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        16.14        21.11        10.62 

  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE 
                        12.345                         13.080 
[1] "0.1 - 115.7 (12.3)" "0.0 - 122.3 (13.1)"
[1] "hr=" "1.2"
D86V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(18Q12.2) MUTATED         5        6       18       16        39
  DEL PEAK 47(18Q12.2) WILD-TYPE       6       13       30       16        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(18Q12.2) MUTATED          37        19         47         36
  DEL PEAK 47(18Q12.2) WILD-TYPE        47        10         50         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 47(18Q12.2) MUTATED           18       21         2
  DEL PEAK 47(18Q12.2) WILD-TYPE         30       30         2
D86V3, multiclass
            clus
vv           DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  STAGE I                               5                              6
  STAGE IA                              6                             13
  STAGE IB                             18                             30
  STAGE II                             16                             16
  STAGE IIA                            39                             38
  STAGE IIB                            37                             47
  STAGE III                            19                             10
  STAGE IIIA                           47                             50
  STAGE IIIB                           36                             36
  STAGE IIIC                           18                             30
  STAGE IV                             21                             30
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 47(18Q12.2) MUTATED      22  56 156  36
  DEL PEAK 47(18Q12.2) WILD-TYPE    31  70 124  88
D86V4, multiclass
       clus
vv      DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  T0+T1                           22                             31
  T2                              56                             70
  T3                             156                            124
  T4                              36                             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 47(18Q12.2) MUTATED    87  88  48  42
  DEL PEAK 47(18Q12.2) WILD-TYPE 113  94  48  55
D86V5, multiclass
    clus
vv   DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  N0                           87                            113
  N1                           88                             94
  N2                           48                             48
  N3                           42                             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V6, binary
                                cls
clus                               0   1
  DEL PEAK 47(18Q12.2) MUTATED   235  17
  DEL PEAK 47(18Q12.2) WILD-TYPE 278  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(18Q12.2) MUTATED    235   17
  DEL PEAK 47(18Q12.2) WILD-TYPE  278   22
   clus
vv  DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  0                          235                            278
  1                           17                             22
[1] 2 2
[1] FALSE
D86V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(18Q12.2) MUTATED    74 209
  DEL PEAK 47(18Q12.2) WILD-TYPE 108 218
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(18Q12.2) MUTATED     74  209
  DEL PEAK 47(18Q12.2) WILD-TYPE  108  218
        clus
vv       DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  FEMALE                           74                            108
  MALE                            209                            218
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 47(18Q12.2) MUTATED                                      27
  DEL PEAK 47(18Q12.2) WILD-TYPE                                    44
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(18Q12.2) MUTATED                                                       60
  DEL PEAK 47(18Q12.2) WILD-TYPE                                                    102
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(18Q12.2) MUTATED                                                                  38
  DEL PEAK 47(18Q12.2) WILD-TYPE                                                                43
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 47(18Q12.2) MUTATED                                                 41
  DEL PEAK 47(18Q12.2) WILD-TYPE                                               37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 47(18Q12.2) MUTATED                                                          6
  DEL PEAK 47(18Q12.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 47(18Q12.2) MUTATED                                                           2
  DEL PEAK 47(18Q12.2) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 47(18Q12.2) MUTATED                                          4
  DEL PEAK 47(18Q12.2) WILD-TYPE                                        9
D86V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 47(18Q12.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      60
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           38
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 47(18Q12.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V9, binary
                                cls
clus                               0   1
  DEL PEAK 47(18Q12.2) MUTATED     2 281
  DEL PEAK 47(18Q12.2) WILD-TYPE   4 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(18Q12.2) MUTATED      2  281
  DEL PEAK 47(18Q12.2) WILD-TYPE    4  322
     clus
vv    DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  NO                             2                              4
  YES                          281                            322
[1] 2 2
[1] FALSE
D86V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(18Q12.2) MUTATED   136  10   6   9
  DEL PEAK 47(18Q12.2) WILD-TYPE 211   8  13  16
D86V11, multiclass
    clus
vv   DEL PEAK 47(18Q12.2) MUTATED DEL PEAK 47(18Q12.2) WILD-TYPE
  R0                          136                            211
  R1                           10                              8
  R2                            6                             13
  RX                            9                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(18Q12.2) MUTATED      63                         4
  DEL PEAK 47(18Q12.2) WILD-TYPE    66                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 47(18Q12.2) MUTATED                                           0
  DEL PEAK 47(18Q12.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 47(18Q12.2) MUTATED     175
  DEL PEAK 47(18Q12.2) WILD-TYPE   210
D86V13, multiclass
                                           clus
vv                                          DEL PEAK 47(18Q12.2) MUTATED
  ASIAN                                                               63
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              175
                                           clus
vv                                          DEL PEAK 47(18Q12.2) WILD-TYPE
  ASIAN                                                                 66
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V14, binary
                                cls
clus                               0   1
  DEL PEAK 47(18Q12.2) MUTATED     4 169
  DEL PEAK 47(18Q12.2) WILD-TYPE   3 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(18Q12.2) MUTATED      4  169
  DEL PEAK 47(18Q12.2) WILD-TYPE    3  225
                        clus
vv                       DEL PEAK 47(18Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          169
                        clus
vv                       DEL PEAK 47(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 48(18Q21.2) MUTATION ANALYSIS
D87V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(18Q21.2) MUTATED   185 113
  DEL PEAK 48(18Q21.2) WILD-TYPE 169 108
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                           298                            277 
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                           113                            108 
$`DEL PEAK 48(18Q21.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94        16.24        32.45         7.69         0.85         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
       18.64         3.88         0.53         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 
       14.50        12.16        68.02         3.68        42.77        25.41 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H 
       23.18        31.56        25.22        24.03         3.16         0.30 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        8.94        24.00         3.68         4.70        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        3.32         7.17         3.16         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        6.94         2.60         3.95         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       35.97        12.92        13.48        16.47        13.55        13.22 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.36        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.59        22.39         0.10        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-M9-A5M8 
       13.22         4.47        12.33        25.25        12.23        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ 
        5.16         7.82         8.02         7.59        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
       53.95         9.30         2.89         1.45        12.69         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       20.02         5.29         4.80         9.27        18.81        19.96 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G 
       22.82        12.43        18.31         8.12        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91        10.16         3.42         2.66        19.73 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       11.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
        6.18         9.57        17.29        13.68        19.33        26.10 
TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       12.16        35.24        15.42        28.01        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        3.45         9.07        11.44        12.95         2.66        16.31 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8483 
        7.40        22.19         0.95        14.04         3.32         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 
       20.22         1.12        15.81         0.49        15.81         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       15.68         8.22        10.68        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI 
        1.48        12.89         0.66        13.51        20.42        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
        0.13         3.42        12.43        11.61        12.20         3.02 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 
       27.02         7.99         8.05        54.08         4.01        47.05 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 
       18.97         7.07        12.00        22.98        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5579 
        1.02        12.03         4.01        69.04        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       19.13        20.55        18.54        13.35        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       15.98        12.33        24.72        19.50        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
       21.14        14.27        16.44        15.16        11.24         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         7.40         0.62         7.99        16.24 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 
       11.38        19.53        14.07        22.29        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
        0.56         5.52         0.23         5.92        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP 
       10.62        24.30        12.30        22.75        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.25         2.10        12.95        23.84        12.30         9.67 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
        3.45        18.81        18.38         5.19         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         5.56         1.81        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        20.15        37.64        45.67        18.21         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 
        6.08         9.24        16.67        37.91       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        18.48        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK 
       21.73         7.73        16.31        22.19         2.50        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       13.35        27.35        61.22         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D 
        9.73        52.24         9.04         2.01         4.54        64.18 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        22.09        18.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        26.04        12.43         0.79 

$`DEL PEAK 48(18Q21.2) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        5.92         4.21         6.21        33.27        20.09        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       20.12         9.30        17.03        12.82        14.86         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC 
      122.10        44.75        60.39        41.52        21.70         6.28 
TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ 
       30.25         4.31        19.99        47.93        18.35         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
       58.59         7.13         8.71        25.12         0.36         7.40 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U 
        7.76         5.49        46.09         5.92        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10         0.10        12.49        12.76        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO 
       11.54        10.52        12.00        12.03        13.18         0.13 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC 
        5.06        14.70         7.04        15.78        20.38         3.42 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       15.35         4.44         1.55        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-Z6-A8JE TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 
       42.87        11.24         2.10        26.70         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        7.43        18.35        30.90         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.87        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 
       12.82         9.21        24.76        23.93        18.15        12.43 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49        14.43         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 
        9.60        20.55         8.05         0.56         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50        13.08         0.26        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        4.31        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        3.72        25.18         9.21        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
        6.28         7.53        11.54        16.44        12.56         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL 
       12.82        19.36         0.46        20.65         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
        5.13         2.83         0.16         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        9.34        11.31         6.58         0.10        12.62        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       15.95         1.02        14.01        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       21.99         0.00         9.01         6.97         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-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       21.07         7.99        12.66        18.84        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 
       15.22        12.79        10.55        11.31        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       20.91         5.92        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
       11.44         8.38         4.34         7.13        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-A5NB TCGA-HJ-7597 
       21.27         3.48        59.54         5.03        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 
        1.51        14.27        12.59        11.41         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.10         6.51        10.19         0.26        19.36         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.81        27.42        21.21         3.39         5.36        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       12.59         6.51         7.82         3.72        19.73         9.86 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       61.25         4.60        11.05         8.61         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04         5.46        13.02        34.45        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       28.96        34.29        46.26        12.79         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
       65.16        36.69        11.70        11.93        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       22.68         7.36        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
        2.66        40.08        28.41        54.12        16.14        21.11 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE 
                         12.43                          12.82 
[1] "0.1 - 115.7 (12.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D87V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(18Q21.2) MUTATED         6        6       22       17        41
  DEL PEAK 48(18Q21.2) WILD-TYPE       5       13       26       15        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(18Q21.2) MUTATED          43        20         51         38
  DEL PEAK 48(18Q21.2) WILD-TYPE        41         9         46         34
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 48(18Q21.2) MUTATED           23       23         2
  DEL PEAK 48(18Q21.2) WILD-TYPE         25       28         2
D87V3, multiclass
            clus
vv           DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                              6                             13
  STAGE IB                             22                             26
  STAGE II                             17                             15
  STAGE IIA                            41                             36
  STAGE IIB                            43                             41
  STAGE III                            20                              9
  STAGE IIIA                           51                             46
  STAGE IIIB                           38                             34
  STAGE IIIC                           23                             25
  STAGE IV                             23                             28
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 48(18Q21.2) MUTATED      26  63 165  45
  DEL PEAK 48(18Q21.2) WILD-TYPE    27  63 115  79
D87V4, multiclass
       clus
vv      DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  T0+T1                           26                             27
  T2                              63                             63
  T3                             165                            115
  T4                              45                             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 48(18Q21.2) MUTATED    96  99  49  49
  DEL PEAK 48(18Q21.2) WILD-TYPE 104  83  47  48
D87V5, multiclass
    clus
vv   DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  N0                           96                            104
  N1                           99                             83
  N2                           49                             47
  N3                           49                             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"
D87V6, binary
                                cls
clus                               0   1
  DEL PEAK 48(18Q21.2) MUTATED   260  19
  DEL PEAK 48(18Q21.2) WILD-TYPE 253  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(18Q21.2) MUTATED    260   19
  DEL PEAK 48(18Q21.2) WILD-TYPE  253   20
   clus
vv  DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  0                          260                            253
  1                           19                             20
[1] 2 2
[1] FALSE
D87V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(18Q21.2) MUTATED    82 231
  DEL PEAK 48(18Q21.2) WILD-TYPE 100 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(18Q21.2) MUTATED     82  231
  DEL PEAK 48(18Q21.2) WILD-TYPE  100  196
        clus
vv       DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  FEMALE                           82                            100
  MALE                            231                            196
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 48(18Q21.2) MUTATED                                      28
  DEL PEAK 48(18Q21.2) WILD-TYPE                                    43
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(18Q21.2) MUTATED                                                       70
  DEL PEAK 48(18Q21.2) WILD-TYPE                                                     92
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(18Q21.2) MUTATED                                                                  44
  DEL PEAK 48(18Q21.2) WILD-TYPE                                                                37
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 48(18Q21.2) MUTATED                                                 44
  DEL PEAK 48(18Q21.2) WILD-TYPE                                               34
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 48(18Q21.2) MUTATED                                                          6
  DEL PEAK 48(18Q21.2) WILD-TYPE                                                       15
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 48(18Q21.2) MUTATED                                                           4
  DEL PEAK 48(18Q21.2) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 48(18Q21.2) MUTATED                                          5
  DEL PEAK 48(18Q21.2) WILD-TYPE                                        8
D87V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 48(18Q21.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      70
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     5
                                                                   clus
vv                                                                  DEL PEAK 48(18Q21.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         43
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        92
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V9, binary
                                cls
clus                               0   1
  DEL PEAK 48(18Q21.2) MUTATED     2 311
  DEL PEAK 48(18Q21.2) WILD-TYPE   4 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(18Q21.2) MUTATED      2  311
  DEL PEAK 48(18Q21.2) WILD-TYPE    4  292
     clus
vv    DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  NO                             2                              4
  YES                          311                            292
[1] 2 2
[1] FALSE
D87V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(18Q21.2) MUTATED   156  11   7  10
  DEL PEAK 48(18Q21.2) WILD-TYPE 191   7  12  15
D87V11, multiclass
    clus
vv   DEL PEAK 48(18Q21.2) MUTATED DEL PEAK 48(18Q21.2) WILD-TYPE
  R0                          156                            191
  R1                           11                              7
  R2                            7                             12
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(18Q21.2) MUTATED      69                         3
  DEL PEAK 48(18Q21.2) WILD-TYPE    60                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(18Q21.2) MUTATED                                           0
  DEL PEAK 48(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 48(18Q21.2) MUTATED     198
  DEL PEAK 48(18Q21.2) WILD-TYPE   187
D87V13, multiclass
                                           clus
vv                                          DEL PEAK 48(18Q21.2) MUTATED
  ASIAN                                                               69
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              198
                                           clus
vv                                          DEL PEAK 48(18Q21.2) WILD-TYPE
  ASIAN                                                                 60
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V14, binary
                                cls
clus                               0   1
  DEL PEAK 48(18Q21.2) MUTATED     5 191
  DEL PEAK 48(18Q21.2) WILD-TYPE   2 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(18Q21.2) MUTATED      5  191
  DEL PEAK 48(18Q21.2) WILD-TYPE    2  203
                        clus
vv                       DEL PEAK 48(18Q21.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          191
                        clus
vv                       DEL PEAK 48(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 49(19P13.3) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 49(19P13.3) MUTATED   134  96
  DEL PEAK 49(19P13.3) WILD-TYPE 220 125
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                           230                            345 
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                            96                            125 
$`DEL PEAK 49(19P13.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       25.78        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L 
        8.94        16.24         4.21         2.63         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FD 
       17.03         0.79        23.41         4.67        44.75        68.02 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        23.18        30.25         4.31        24.00         3.68 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        47.93         3.32         7.17         1.38        58.59 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.43         2.60         3.95         2.66        35.97        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       16.47        13.55         5.49         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S 
       46.09        10.36        10.45        12.66         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 
       15.35        13.25        12.46        12.49        12.76         0.10 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.33         4.47        12.33        10.52        12.23        13.18 
TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        0.13         8.02         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
       53.95        15.78         2.89         1.45        12.69         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW 
        4.80         9.27        18.81        19.96        12.43         8.12 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       42.87        46.19         9.17         2.10         2.66        19.73 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 
       19.56        11.01         9.44         6.61        19.33         9.17 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
        9.21        35.24        28.01        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8369 
        0.69        12.95         2.66        16.31         2.20        14.04 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ 
       14.79         9.21        20.22        11.54        10.68        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
        1.48        12.89         0.72        20.65         1.15         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        0.13         0.16         0.13         0.13         3.42         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       11.31        12.43        11.61        12.20        20.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
       54.08         4.01        29.98        19.07        21.99        18.97 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       22.98        36.00        12.03        15.02         4.01        69.04 
TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       12.66        18.84        13.35        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8578 TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 
       11.31        19.50        21.14         2.96        15.65         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
       72.23        11.38        14.07        17.06         0.56         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       12.59        11.77         8.98         6.25         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       23.84        12.30         9.67        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38         5.19         1.41         6.74        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G 
        5.56         1.81         2.53         5.56        60.56        20.15 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        45.67        18.21         6.08         9.24         8.61 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        5.13        37.91         8.94         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.46        13.25        13.02        18.48        35.24        34.45 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
        7.73        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       27.35         1.71        36.16         9.50         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-AA64 
        9.04         2.01         4.54         5.72        21.04        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       40.08        32.94        17.13        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 49(19P13.3) WILD-TYPE`
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
        5.92        32.45         7.69         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 
        0.85        20.78        20.12        18.64         9.30        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
        9.96        14.86        14.50        12.16       122.10        60.39 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        25.41        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG 
       24.03         6.28         3.16         0.30         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       19.99        21.01        18.35         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         6.94         8.71        25.12         0.36         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        55.50        13.48        13.22         7.76        21.37 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49V 
       27.12        83.24         5.92        12.43        13.41         0.10 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
        0.10        12.59        12.59        22.39        15.52        11.54 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FU 
       13.22        25.25        12.00        12.03        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BV 
        7.82         7.59        14.70         9.30         7.00        20.02 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
       20.38         5.29        15.35         4.44        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
       18.31        28.11        30.71        18.18        15.06        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK 
       15.91        10.16         3.42        26.70        11.70         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       32.94        12.82        24.76        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32        12.43         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        19.50        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19        17.52         0.95        26.33         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        19.17         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        15.81         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53         0.49        15.81        16.44         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68         8.22        12.56        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
        0.66        19.36        13.51         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8528 
       11.57         5.13         2.83        13.18         0.07         0.10 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.10         0.10         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 
        3.02        27.02        15.95         1.02         8.05        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       47.05        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
      105.07        28.96        79.07        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       12.36        11.93        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 
       17.85        17.19        10.26        15.22        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        17.19        18.21        14.66        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-A747 TCGA-D7-A748 
       11.24        11.31        11.44         9.76         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13         0.62        16.24        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        5.52         0.23        18.08        26.47         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-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ 
        0.26        19.36         8.88         8.81         3.45         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-MX-A5UG 
       13.08         6.44         6.51         7.82        13.51         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73         9.86         8.52        61.25         4.60        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-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       57.44        35.61        16.87        19.04        21.73        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 
       18.74        20.81        22.68         7.36        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA69 
       64.18         2.66        42.54        11.24        22.09        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZA-A8F6 
       29.98        54.12        10.62 

  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE 
                        12.315                         13.450 
[1] "0.1 - 72.2 (12.3)"  "0.0 - 122.3 (13.4)"
[1] "hr=" "1.3"
D88V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(19P13.3) MUTATED         4        8       17       13        27
  DEL PEAK 49(19P13.3) WILD-TYPE       7       11       31       19        50
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(19P13.3) MUTATED          36        16         38         26
  DEL PEAK 49(19P13.3) WILD-TYPE        48        13         59         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 49(19P13.3) MUTATED           18       19         3
  DEL PEAK 49(19P13.3) WILD-TYPE         30       32         1
D88V3, multiclass
            clus
vv           DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  STAGE I                               4                              7
  STAGE IA                              8                             11
  STAGE IB                             17                             31
  STAGE II                             13                             19
  STAGE IIA                            27                             50
  STAGE IIB                            36                             48
  STAGE III                            16                             13
  STAGE IIIA                           38                             59
  STAGE IIIB                           26                             46
  STAGE IIIC                           18                             30
  STAGE IV                             19                             32
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 49(19P13.3) MUTATED      20  48 123  36
  DEL PEAK 49(19P13.3) WILD-TYPE    33  78 157  88
D88V4, multiclass
       clus
vv      DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  T0+T1                           20                             33
  T2                              48                             78
  T3                             123                            157
  T4                              36                             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 49(19P13.3) MUTATED    72  78  36  38
  DEL PEAK 49(19P13.3) WILD-TYPE 128 104  60  59
D88V5, multiclass
    clus
vv   DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  N0                           72                            128
  N1                           78                            104
  N2                           36                             60
  N3                           38                             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"
D88V6, binary
                                cls
clus                               0   1
  DEL PEAK 49(19P13.3) MUTATED   199  15
  DEL PEAK 49(19P13.3) WILD-TYPE 314  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(19P13.3) MUTATED    199   15
  DEL PEAK 49(19P13.3) WILD-TYPE  314   24
   clus
vv  DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  0                          199                            314
  1                           15                             24
[1] 2 2
[1] FALSE
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 49(19P13.3) MUTATED    55 187
  DEL PEAK 49(19P13.3) WILD-TYPE 127 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(19P13.3) MUTATED     55  187
  DEL PEAK 49(19P13.3) WILD-TYPE  127  240
        clus
vv       DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  FEMALE                           55                            127
  MALE                            187                            240
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 49(19P13.3) MUTATED                                      15
  DEL PEAK 49(19P13.3) WILD-TYPE                                    56
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(19P13.3) MUTATED                                                       53
  DEL PEAK 49(19P13.3) WILD-TYPE                                                    109
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(19P13.3) MUTATED                                                                  41
  DEL PEAK 49(19P13.3) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 49(19P13.3) MUTATED                                                 34
  DEL PEAK 49(19P13.3) WILD-TYPE                                               44
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 49(19P13.3) MUTATED                                                          5
  DEL PEAK 49(19P13.3) WILD-TYPE                                                       16
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 49(19P13.3) MUTATED                                                           4
  DEL PEAK 49(19P13.3) WILD-TYPE                                                         4
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 49(19P13.3) MUTATED                                          4
  DEL PEAK 49(19P13.3) WILD-TYPE                                        9
D88V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 49(19P13.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     4
                                                                   clus
vv                                                                  DEL PEAK 49(19P13.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       109
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V9, binary
                                cls
clus                               0   1
  DEL PEAK 49(19P13.3) MUTATED     5 237
  DEL PEAK 49(19P13.3) WILD-TYPE   1 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(19P13.3) MUTATED      5  237
  DEL PEAK 49(19P13.3) WILD-TYPE    1  366
     clus
vv    DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  NO                             5                              1
  YES                          237                            366
[1] 2 2
[1] FALSE
D88V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 49(19P13.3) MUTATED   122   4   9   6
  DEL PEAK 49(19P13.3) WILD-TYPE 225  14  10  19
D88V11, multiclass
    clus
vv   DEL PEAK 49(19P13.3) MUTATED DEL PEAK 49(19P13.3) WILD-TYPE
  R0                          122                            225
  R1                            4                             14
  R2                            9                             10
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(19P13.3) MUTATED      61                         7
  DEL PEAK 49(19P13.3) WILD-TYPE    68                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 49(19P13.3) MUTATED                                           1
  DEL PEAK 49(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 49(19P13.3) MUTATED     136
  DEL PEAK 49(19P13.3) WILD-TYPE   249
D88V13, multiclass
                                           clus
vv                                          DEL PEAK 49(19P13.3) MUTATED
  ASIAN                                                               61
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              136
                                           clus
vv                                          DEL PEAK 49(19P13.3) WILD-TYPE
  ASIAN                                                                 68
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V14, binary
                                cls
clus                               0   1
  DEL PEAK 49(19P13.3) MUTATED     2 141
  DEL PEAK 49(19P13.3) WILD-TYPE   5 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(19P13.3) MUTATED      2  141
  DEL PEAK 49(19P13.3) WILD-TYPE    5  253
                        clus
vv                       DEL PEAK 49(19P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK 49(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 50(19Q13.11) MUTATION ANALYSIS
D89V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 50(19Q13.11) MUTATED    71  44
  DEL PEAK 50(19Q13.11) WILD-TYPE 283 177
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                            115                             460 
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                             44                             177 
$`DEL PEAK 50(19Q13.11) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A50L 
       25.78        14.30         4.21         7.69         2.63         0.53 
TCGA-IG-A6QS TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A43E TCGA-L5-A43J TCGA-L5-A4OM 
        9.96        68.02        42.77        30.25         4.31        47.93 
TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 
        7.17        58.59         4.90         7.43         6.94         3.95 
TCGA-L5-A8NF TCGA-L5-A8NL TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V 
        2.66        13.22        12.66         0.10        13.15         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HX 
       12.46        12.59        12.49         4.47        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-R6-A8WC 
       12.03        13.18         8.02         7.04        15.78         1.45 
TCGA-VR-A8EO TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D TCGA-Z6-AAPN 
       18.81         8.12        18.18        42.87         9.17         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 
       19.73        11.01         9.44         6.61         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
       15.42        28.73         3.45        11.44         0.69         2.66 
TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 
       14.04        11.54         1.48         1.15         3.25        13.15 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 
        0.07         0.13         0.13         3.42        11.31        20.02 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        4.01        18.97        12.03        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 
       12.79        11.31        19.50        13.78        11.31         2.96 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH 
       15.65         0.62        17.06         0.56         5.92        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RI 
        8.98         6.25        12.95        23.84        27.42        18.38 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A8MW 
       12.59         5.56         1.81        37.64        45.67        37.91 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PH TCGA-VQ-A8PK 
        5.46        13.02        18.48        32.48        12.79        17.85 
TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       27.35        18.74        36.16         9.50        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J 
        4.54        64.18        21.04        17.13        16.14        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 50(19Q13.11) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24        32.45         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       20.78        20.12        18.64         3.88         9.30        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        44.75        60.39         3.68        41.52 
TCGA-JY-A938 TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       25.41        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF 
        6.28         3.16         0.30         8.94        24.00         3.68 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        21.01        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88T TCGA-L5-A88V 
        1.38         3.16        29.00         7.13         8.71         2.60 
TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NG 
       25.12         0.36         7.40         3.02        55.50        35.97 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
       21.37         8.71        13.41        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.36         5.92        10.45        12.43        13.41 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       15.35        13.25         0.10        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
        0.10        15.52        11.54        12.33        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW 
       10.52        12.00         0.13        33.11         5.16         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59         5.06        14.70        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW 
        9.30         2.89        12.69         7.00        20.02        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42         4.80        15.35         9.27         4.44 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX 
       19.96        22.82        12.43         1.55        18.31        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       30.71        46.19        15.06        11.24        15.91        10.16 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        3.42         2.10        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        6.97         4.64         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       28.01        18.15        15.32        12.43         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       18.71        17.49        14.43        12.26         9.60        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        12.95        16.31         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        13.45         6.28         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       13.64        11.57         5.13         2.83        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 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-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.10         0.13         0.10         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.61         6.58        12.20         0.10        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       13.35        15.98        10.55        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        15.16        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         8.38         4.34         7.40         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.99        16.24        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.51        10.19         0.26         2.10        19.36        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-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-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.51         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       60.56        20.15         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        8.61         5.13        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79        13.25        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        34.45        27.88         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       46.26        16.31        22.19         2.50         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       20.81        22.68         1.71         7.36         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         6.58         5.72         2.66        42.54        11.24 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       22.09        18.41        40.08        28.41        32.94        29.98 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        12.43        10.62 

  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                          68.02                          122.30 
  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE 
                         12.030                          13.015 
[1] "0.1 - 68.0 (12.0)"  "0.0 - 122.3 (13.0)"
[1] "hr=" "1.2"
D89V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(19Q13.11) MUTATED         2        4        7        7        16
  DEL PEAK 50(19Q13.11) WILD-TYPE       9       15       41       25        61
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(19Q13.11) MUTATED          15         6         18         15
  DEL PEAK 50(19Q13.11) WILD-TYPE        69        23         79         57
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 50(19Q13.11) MUTATED            9       11         2
  DEL PEAK 50(19Q13.11) WILD-TYPE         39       40         2
D89V3, multiclass
            clus
vv           DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  STAGE I                                2                               9
  STAGE IA                               4                              15
  STAGE IB                               7                              41
  STAGE II                               7                              25
  STAGE IIA                             16                              61
  STAGE IIB                             15                              69
  STAGE III                              6                              23
  STAGE IIIA                            18                              79
  STAGE IIIB                            15                              57
  STAGE IIIC                             9                              39
  STAGE IV                              11                              40
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 50(19Q13.11) MUTATED       8  22  64  19
  DEL PEAK 50(19Q13.11) WILD-TYPE    45 104 216 105
D89V4, multiclass
       clus
vv      DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  T0+T1                             8                              45
  T2                               22                             104
  T3                               64                             216
  T4                               19                             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 50(19Q13.11) MUTATED    36  36  16  23
  DEL PEAK 50(19Q13.11) WILD-TYPE 164 146  80  74
D89V5, multiclass
    clus
vv   DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  N0                            36                             164
  N1                            36                             146
  N2                            16                              80
  N3                            23                              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"
D89V6, binary
                                 cls
clus                                0   1
  DEL PEAK 50(19Q13.11) MUTATED    96  11
  DEL PEAK 50(19Q13.11) WILD-TYPE 417  28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(19Q13.11) MUTATED     96   11
  DEL PEAK 50(19Q13.11) WILD-TYPE  417   28
   clus
vv  DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  0                            96                             417
  1                            11                              28
[1] 2 2
[1] FALSE
D89V7, binary
                                 cls
clus                                0   1
  DEL PEAK 50(19Q13.11) MUTATED    29  89
  DEL PEAK 50(19Q13.11) WILD-TYPE 153 338
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(19Q13.11) MUTATED     29   89
  DEL PEAK 50(19Q13.11) WILD-TYPE  153  338
        clus
vv       DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  FEMALE                            29                             153
  MALE                              89                             338
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 50(19Q13.11) MUTATED                                       5
  DEL PEAK 50(19Q13.11) WILD-TYPE                                    66
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(19Q13.11) MUTATED                                                       24
  DEL PEAK 50(19Q13.11) WILD-TYPE                                                    138
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(19Q13.11) MUTATED                                                                  17
  DEL PEAK 50(19Q13.11) WILD-TYPE                                                                64
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 50(19Q13.11) MUTATED                                                 25
  DEL PEAK 50(19Q13.11) WILD-TYPE                                               53
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 50(19Q13.11) MUTATED                                                          1
  DEL PEAK 50(19Q13.11) WILD-TYPE                                                       20
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 50(19Q13.11) MUTATED                                                           2
  DEL PEAK 50(19Q13.11) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 50(19Q13.11) MUTATED                                          1
  DEL PEAK 50(19Q13.11) WILD-TYPE                                       12
D89V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 50(19Q13.11) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      1
                                                                   clus
vv                                                                  DEL PEAK 50(19Q13.11) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          66
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V9, binary
                                 cls
clus                                0   1
  DEL PEAK 50(19Q13.11) MUTATED     1 117
  DEL PEAK 50(19Q13.11) WILD-TYPE   5 486
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(19Q13.11) MUTATED      1  117
  DEL PEAK 50(19Q13.11) WILD-TYPE    5  486
     clus
vv    DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  NO                              1                               5
  YES                           117                             486
[1] 2 2
[1] FALSE
D89V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 50(19Q13.11) MUTATED    60   1   5   3
  DEL PEAK 50(19Q13.11) WILD-TYPE 287  17  14  22
D89V11, multiclass
    clus
vv   DEL PEAK 50(19Q13.11) MUTATED DEL PEAK 50(19Q13.11) WILD-TYPE
  R0                            60                             287
  R1                             1                              17
  R2                             5                              14
  RX                             3                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 50(19Q13.11) MUTATED      30                         4
  DEL PEAK 50(19Q13.11) WILD-TYPE    99                         9
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 50(19Q13.11) MUTATED                                           0
  DEL PEAK 50(19Q13.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 50(19Q13.11) MUTATED      71
  DEL PEAK 50(19Q13.11) WILD-TYPE   314
D89V13, multiclass
                                           clus
vv                                          DEL PEAK 50(19Q13.11) MUTATED
  ASIAN                                                                30
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                71
                                           clus
vv                                          DEL PEAK 50(19Q13.11) WILD-TYPE
  ASIAN                                                                  99
  BLACK OR AFRICAN AMERICAN                                               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V14, binary
                                 cls
clus                                0   1
  DEL PEAK 50(19Q13.11) MUTATED     1  72
  DEL PEAK 50(19Q13.11) WILD-TYPE   6 322
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(19Q13.11) MUTATED      1   72
  DEL PEAK 50(19Q13.11) WILD-TYPE    6  322
                        clus
vv                       DEL PEAK 50(19Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            72
                        clus
vv                       DEL PEAK 50(19Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             322
[1] 2 2
[1] FALSE

Clustering(90) Variable = DEL PEAK 51(20P12.1) MUTATION ANALYSIS
D90V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 51(20P12.1) MUTATED    39  29
  DEL PEAK 51(20P12.1) WILD-TYPE 315 192
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                            68                            507 
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                            29                            192 
$`DEL PEAK 51(20P12.1) MUTATED`
TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A938 
       14.30         3.88        44.75        68.02        42.77        25.41 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NE TCGA-L5-A8NF 
        8.94         3.68        32.61         3.32        55.50         2.66 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A6VZ 
       16.47        13.22         8.71        13.41        83.24        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW TCGA-LN-A7HY 
       10.45        12.66        13.41        12.46        12.00        12.03 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EQ 
        5.06        29.59        53.95        12.69        20.38        22.82 
TCGA-VR-A8Q7 TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7723 
       42.87        19.73         6.18        17.29        26.10        28.73 
TCGA-BR-8289 TCGA-BR-A4IY TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A48C 
        2.66        12.89        20.65        13.64         0.07        11.61 
TCGA-CG-4301 TCGA-CG-5717 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
        3.02         6.97        15.02        20.55        17.19        10.26 
TCGA-D7-8575 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 TCGA-HU-A4GF 
       18.21        14.66         0.62        16.24        14.17        25.81 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-AB1V TCGA-IP-7968 TCGA-RD-A8MW TCGA-SW-A7EA 
        5.36         1.41         7.82         2.53        37.91        19.04 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A925 
        5.46        18.48        32.48        46.26        17.85         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6D 
       40.08        17.13 

$`DEL PEAK 51(20P12.1) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF 
        8.94        16.24         4.21        32.45         7.69         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        20.09         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       18.64         9.30         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       12.82         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
      122.10        60.39         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       31.56        25.22        24.03         6.28         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4OJ 
        0.30         4.31        24.00         4.70        19.99        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         7.17         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        2.60        25.12         0.36         7.40         3.95         3.02 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       35.97        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49N 
       21.37        27.12        52.57        46.09         5.92        12.43 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 
       25.25        10.52        12.23        13.18         0.13        33.11 
TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
        5.16         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89         1.45         7.00 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.02         5.29         3.42         4.80        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        4.44        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE 
       11.24         9.17        15.91        10.16         3.42         2.10 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        39.12         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        12.95        16.31         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         9.86        15.68         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56        13.87         7.53         6.08        22.26         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-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-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-8532 TCGA-CD-8533 
        0.10         0.13         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-A48A 
        0.13         0.10         3.42         9.34        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20         0.10        12.62        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-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        0.00         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
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-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       15.65         8.38         4.34         7.40         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        23.84        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.81        27.42        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.19        13.08         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51         5.56         1.81        13.51         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 
       20.15        37.64         3.72        19.73         9.86        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       35.24        21.73        34.45        27.88         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       27.35        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       36.16         7.36         9.50         9.73        52.24         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
        2.01        55.43         6.58         5.72        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
        2.66        42.54        11.24        22.09        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        29.98        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE 
                        14.235                         12.590 
[1] "0.1 - 83.2 (14.2)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D90V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(20P12.1) MUTATED         1        2        6        2         9
  DEL PEAK 51(20P12.1) WILD-TYPE      10       17       42       30        68
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(20P12.1) MUTATED          10         6         12          8
  DEL PEAK 51(20P12.1) WILD-TYPE        74        23         85         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 51(20P12.1) MUTATED            4        4         1
  DEL PEAK 51(20P12.1) WILD-TYPE         44       47         3
D90V3, multiclass
            clus
vv           DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  STAGE I                               1                             10
  STAGE IA                              2                             17
  STAGE IB                              6                             42
  STAGE II                              2                             30
  STAGE IIA                             9                             68
  STAGE IIB                            10                             74
  STAGE III                             6                             23
  STAGE IIIA                           12                             85
  STAGE IIIB                            8                             64
  STAGE IIIC                            4                             44
  STAGE IV                              4                             47
  STAGE IVA                             1                              3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 51(20P12.1) MUTATED       6  16  35   9
  DEL PEAK 51(20P12.1) WILD-TYPE    47 110 245 115
D90V4, multiclass
       clus
vv      DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  T0+T1                            6                             47
  T2                              16                            110
  T3                              35                            245
  T4                               9                            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"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 51(20P12.1) MUTATED    23  22  11  10
  DEL PEAK 51(20P12.1) WILD-TYPE 177 160  85  87
D90V5, multiclass
    clus
vv   DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  N0                           23                            177
  N1                           22                            160
  N2                           11                             85
  N3                           10                             87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V6, binary
                                cls
clus                               0   1
  DEL PEAK 51(20P12.1) MUTATED    54   4
  DEL PEAK 51(20P12.1) WILD-TYPE 459  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 51(20P12.1) MUTATED     54    4
  DEL PEAK 51(20P12.1) WILD-TYPE  459   35
   clus
vv  DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  0                           54                            459
  1                            4                             35
[1] 2 2
[1] FALSE
D90V7, binary
                                cls
clus                               0   1
  DEL PEAK 51(20P12.1) MUTATED    19  51
  DEL PEAK 51(20P12.1) WILD-TYPE 163 376
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 51(20P12.1) MUTATED     19   51
  DEL PEAK 51(20P12.1) WILD-TYPE  163  376
        clus
vv       DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  FEMALE                           19                            163
  MALE                             51                            376
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 51(20P12.1) MUTATED                                       3
  DEL PEAK 51(20P12.1) WILD-TYPE                                    68
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(20P12.1) MUTATED                                                       17
  DEL PEAK 51(20P12.1) WILD-TYPE                                                    145
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(20P12.1) MUTATED                                                                   4
  DEL PEAK 51(20P12.1) WILD-TYPE                                                                77
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 51(20P12.1) MUTATED                                                 10
  DEL PEAK 51(20P12.1) WILD-TYPE                                               68
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 51(20P12.1) MUTATED                                                          2
  DEL PEAK 51(20P12.1) WILD-TYPE                                                       19
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 51(20P12.1) MUTATED                                                           1
  DEL PEAK 51(20P12.1) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 51(20P12.1) MUTATED                                          1
  DEL PEAK 51(20P12.1) WILD-TYPE                                       12
D90V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 51(20P12.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 51(20P12.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         68
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             77
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              68
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V9, binary
                                cls
clus                               0   1
  DEL PEAK 51(20P12.1) MUTATED     2  68
  DEL PEAK 51(20P12.1) WILD-TYPE   4 535
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 51(20P12.1) MUTATED      2   68
  DEL PEAK 51(20P12.1) WILD-TYPE    4  535
     clus
vv    DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  NO                             2                              4
  YES                           68                            535
[1] 2 2
[1] FALSE
D90V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 51(20P12.1) MUTATED    32   1   3   1
  DEL PEAK 51(20P12.1) WILD-TYPE 315  17  16  24
D90V11, multiclass
    clus
vv   DEL PEAK 51(20P12.1) MUTATED DEL PEAK 51(20P12.1) WILD-TYPE
  R0                           32                            315
  R1                            1                             17
  R2                            3                             16
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 51(20P12.1) MUTATED      14                         1
  DEL PEAK 51(20P12.1) WILD-TYPE   115                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 51(20P12.1) MUTATED                                           0
  DEL PEAK 51(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 51(20P12.1) MUTATED      46
  DEL PEAK 51(20P12.1) WILD-TYPE   339
D90V13, multiclass
                                           clus
vv                                          DEL PEAK 51(20P12.1) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               46
                                           clus
vv                                          DEL PEAK 51(20P12.1) WILD-TYPE
  ASIAN                                                                115
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V14, binary
                                cls
clus                               0   1
  DEL PEAK 51(20P12.1) MUTATED     1  38
  DEL PEAK 51(20P12.1) WILD-TYPE   6 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 51(20P12.1) MUTATED      1   38
  DEL PEAK 51(20P12.1) WILD-TYPE    6  356
                        clus
vv                       DEL PEAK 51(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       DEL PEAK 51(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            356
[1] 2 2
[1] FALSE

Clustering(91) Variable = DEL PEAK 52(21Q11.2) MUTATION ANALYSIS
D91V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 52(21Q11.2) MUTATED   160 109
  DEL PEAK 52(21Q11.2) WILD-TYPE 194 112
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                           269                            306 
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                           109                            112 
$`DEL PEAK 52(21Q11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63         5.92        13.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A93C 
        0.79         9.96        12.16       122.10        68.02        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       31.56        24.03         3.16        30.25         0.30         4.31 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OM 
        8.94        24.00         3.68         4.70        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       18.35         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
        7.13         6.94         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW 
        5.49         8.71        13.41        27.12        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.36         5.92        12.43        13.41         0.10        13.15 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 
       13.25         0.10        12.76        22.39         0.10        11.54 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22         4.47        12.33        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 
       13.18        33.11         7.82         8.02         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       29.59         6.35         9.30         2.89         1.45        12.69 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       20.38         4.80         9.27         4.44        18.81        22.82 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        1.55         8.12        28.11        42.87        46.19        11.24 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.10         2.66        19.73        11.70        11.01         9.44 
TCGA-BR-4184 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 
        6.97        13.68        19.33        26.10         9.17        31.20 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 
       35.24        15.42        28.01        28.73        18.71        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8361 
       12.26         9.60         8.05        16.31        15.58        19.50 
TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 
       17.52         4.31        14.04        14.79         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        9.21        20.22        11.54         9.86        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       10.68         7.53        22.26         1.48        12.89         0.72 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 
        0.07         0.07         0.07         0.16         0.13         9.34 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
       11.31        12.43        11.61        12.20        20.02        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
        4.01        47.05        12.03        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5730 
        6.97        36.00         1.02        12.03        65.10         4.01 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       11.93        19.13        20.55        13.35        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       12.79        11.31        12.33        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         7.99        72.23        11.38        19.53 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
        5.52         0.23        26.47         1.51        14.17        12.10 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-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-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.36         5.19         1.41         6.74         5.56         1.81 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
        7.82         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        9.86        45.67        18.21         8.52        61.25         6.08 
TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        9.24       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        21.73         7.73        22.19         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
        1.87        23.41        27.35        64.57        14.33        36.69 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       61.22        18.74        20.81         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        11.24        22.09        18.41        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       29.98        54.12        26.04        12.43         0.79 

$`DEL PEAK 52(21Q11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
        7.69         6.21        20.09         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41        12.82        14.86         4.67        14.50        44.75 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OQ 
       25.22         6.28        19.99        21.01         3.32         1.38 
TCGA-L5-A4OX TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NI 
        7.43         8.71        25.12        55.50        35.97        13.48 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49U 
        7.76        21.37        83.24        10.45        12.66        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 
        0.10        12.46        12.59        12.49        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DQ 
       12.33        25.25        10.52         0.13         5.16         7.59 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       14.70        53.95        15.78         7.00        20.02         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY 
        3.42        15.35        19.96        12.43        18.31        30.71 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.18        15.06         9.17        15.91        10.16         3.42 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       26.70        19.56         9.47         6.61         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 
       15.95        13.87        17.29        39.12        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82         9.21        24.76        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        12.43         3.45         9.07        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69        20.55         0.56        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20         7.40         6.18        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        0.95        26.33         3.32        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       15.85         3.72         1.12        12.79        15.81         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         6.28         7.53         0.49        15.81        16.44 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       12.56        13.87         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
       14.17         0.53        12.82         0.66        19.36        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.10         3.42         6.58         0.10        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        21.99         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        7.07        12.00         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        79.07        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        12.66        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.26        15.22        10.55        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       17.19        18.21        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96         8.38         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       16.24        14.47        21.27         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.56        18.08 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.30         5.59        12.30        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         2.10        12.95        23.84         8.88         8.81 
TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1X 
        3.45        13.08         6.44        12.59         6.51        13.51 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA 
       16.67        40.64       116.38        71.38        16.87        19.04 
TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        35.24        34.45        27.88        32.48        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PO 
       34.29        46.26        16.31         2.50        12.79         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       15.65        13.35        26.24        65.16        11.70        11.93 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       22.68         7.36         6.58         5.72        64.18         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       28.41        32.94        17.13        16.14        21.11        10.62 

  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE 
                        12.330                         12.885 
[1] "0.1 - 122.3 (12.3)" "0.0 - 116.4 (12.9)"
[1] "hr=" "1"  
D91V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(21Q11.2) MUTATED         6        8       25       10        38
  DEL PEAK 52(21Q11.2) WILD-TYPE       5       11       23       22        39
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(21Q11.2) MUTATED          36        15         50         30
  DEL PEAK 52(21Q11.2) WILD-TYPE        48        14         47         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 52(21Q11.2) MUTATED           19       22         2
  DEL PEAK 52(21Q11.2) WILD-TYPE         29       29         2
D91V3, multiclass
            clus
vv           DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                              8                             11
  STAGE IB                             25                             23
  STAGE II                             10                             22
  STAGE IIA                            38                             39
  STAGE IIB                            36                             48
  STAGE III                            15                             14
  STAGE IIIA                           50                             47
  STAGE IIIB                           30                             42
  STAGE IIIC                           19                             29
  STAGE IV                             22                             29
  STAGE IVA                             2                              2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 52(21Q11.2) MUTATED      25  56 136  48
  DEL PEAK 52(21Q11.2) WILD-TYPE    28  70 144  76
D91V4, multiclass
       clus
vv      DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  T0+T1                           25                             28
  T2                              56                             70
  T3                             136                            144
  T4                              48                             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 52(21Q11.2) MUTATED    92  86  48  36
  DEL PEAK 52(21Q11.2) WILD-TYPE 108  96  48  61
D91V5, multiclass
    clus
vv   DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  N0                           92                            108
  N1                           86                             96
  N2                           48                             48
  N3                           36                             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"
D91V6, binary
                                cls
clus                               0   1
  DEL PEAK 52(21Q11.2) MUTATED   230  16
  DEL PEAK 52(21Q11.2) WILD-TYPE 283  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(21Q11.2) MUTATED    230   16
  DEL PEAK 52(21Q11.2) WILD-TYPE  283   23
   clus
vv  DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  0                          230                            283
  1                           16                             23
[1] 2 2
[1] FALSE
D91V7, binary
                                cls
clus                               0   1
  DEL PEAK 52(21Q11.2) MUTATED    84 196
  DEL PEAK 52(21Q11.2) WILD-TYPE  98 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(21Q11.2) MUTATED     84  196
  DEL PEAK 52(21Q11.2) WILD-TYPE   98  231
        clus
vv       DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  FEMALE                           84                             98
  MALE                            196                            231
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 52(21Q11.2) MUTATED                                      23
  DEL PEAK 52(21Q11.2) WILD-TYPE                                    48
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(21Q11.2) MUTATED                                                       61
  DEL PEAK 52(21Q11.2) WILD-TYPE                                                    101
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(21Q11.2) MUTATED                                                                  41
  DEL PEAK 52(21Q11.2) WILD-TYPE                                                                40
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 52(21Q11.2) MUTATED                                                 37
  DEL PEAK 52(21Q11.2) WILD-TYPE                                               41
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 52(21Q11.2) MUTATED                                                          9
  DEL PEAK 52(21Q11.2) WILD-TYPE                                                       12
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 52(21Q11.2) MUTATED                                                           1
  DEL PEAK 52(21Q11.2) WILD-TYPE                                                         7
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 52(21Q11.2) MUTATED                                          8
  DEL PEAK 52(21Q11.2) WILD-TYPE                                        5
D91V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 52(21Q11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     8
                                                                   clus
vv                                                                  DEL PEAK 52(21Q11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       101
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V9, binary
                                cls
clus                               0   1
  DEL PEAK 52(21Q11.2) MUTATED     4 276
  DEL PEAK 52(21Q11.2) WILD-TYPE   2 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(21Q11.2) MUTATED      4  276
  DEL PEAK 52(21Q11.2) WILD-TYPE    2  327
     clus
vv    DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  NO                             4                              2
  YES                          276                            327
[1] 2 2
[1] FALSE
D91V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 52(21Q11.2) MUTATED   145   9   8   6
  DEL PEAK 52(21Q11.2) WILD-TYPE 202   9  11  19
D91V11, multiclass
    clus
vv   DEL PEAK 52(21Q11.2) MUTATED DEL PEAK 52(21Q11.2) WILD-TYPE
  R0                          145                            202
  R1                            9                              9
  R2                            8                             11
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 52(21Q11.2) MUTATED      54                         6
  DEL PEAK 52(21Q11.2) WILD-TYPE    75                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 52(21Q11.2) MUTATED                                           0
  DEL PEAK 52(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 52(21Q11.2) MUTATED     180
  DEL PEAK 52(21Q11.2) WILD-TYPE   205
D91V13, multiclass
                                           clus
vv                                          DEL PEAK 52(21Q11.2) MUTATED
  ASIAN                                                               54
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              180
                                           clus
vv                                          DEL PEAK 52(21Q11.2) WILD-TYPE
  ASIAN                                                                 75
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V14, binary
                                cls
clus                               0   1
  DEL PEAK 52(21Q11.2) MUTATED     4 162
  DEL PEAK 52(21Q11.2) WILD-TYPE   3 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 52(21Q11.2) MUTATED      4  162
  DEL PEAK 52(21Q11.2) WILD-TYPE    3  232
                        clus
vv                       DEL PEAK 52(21Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          162
                        clus
vv                       DEL PEAK 52(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(92) Variable = DEL PEAK 53(21Q22.13) MUTATION ANALYSIS
D92V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 53(21Q22.13) MUTATED   171 111
  DEL PEAK 53(21Q22.13) WILD-TYPE 183 110
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                            282                             293 
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                            111                             110 
$`DEL PEAK 53(21Q22.13) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 
       25.78         7.63        13.94         8.94        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
        0.85        20.78        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A93C 
        0.79         9.96       122.10        44.75        68.02        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       31.56        25.22        24.03         3.16        30.25         0.30 
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OJ 
        4.31         8.94        24.00         4.70        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93         7.17         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z 
        7.13         7.43         6.94         2.60         0.36         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ 
        3.95         3.02         2.66        35.97        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV 
       13.55        13.22         8.71        13.41        27.12        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09        10.36         5.92        12.43        13.41        13.15 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
        0.10        12.76         0.10        12.33        13.22        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.00        12.23        12.03        13.18        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        8.02         7.59         5.06         7.04        29.59         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE 
        9.30         2.89         1.45        12.69         3.42         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         4.44        18.81        22.82        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        28.11        18.18        42.87        46.19        11.24 
TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
        9.17         2.10         2.66        19.73        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
        9.44         6.97        18.35        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
        9.17        31.20        35.24        15.42        28.01        28.73 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       18.71        14.43        11.44         9.60         8.05        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
       15.58         7.40        19.50        17.52         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        25.18         9.21        11.54        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        15.68        10.68         7.53        22.26         1.48 
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        11.31        12.43        11.61        12.20 
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        69.04        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        11.38        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        23.84        12.30         9.67        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36         5.19         1.41         6.74 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.51         5.56         1.81         7.82         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        37.64         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52        61.25         6.08         9.24        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA 
       37.91       115.69        57.44         8.94        35.61        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.45         7.73        46.26        22.19        17.85         1.87 
TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K 
       23.41        27.35        64.57        14.33        36.69        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        20.81         1.71        36.16         9.73        52.24 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        2.01        55.43         4.54        64.18        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        22.09        18.41        40.08        32.94        29.98 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        54.12        16.14        21.11        12.43         0.79 

$`DEL PEAK 53(21Q22.13) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ 
       31.27        14.30        58.55         5.92        16.24         4.21 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
        7.69         6.21        20.09         2.63         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82        14.86         4.67        14.50        12.16 
TCGA-JY-A6FB TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A939 
       60.39         3.68        41.52        42.77        25.41        21.70 
TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        6.28         3.68        19.99        18.35         3.32         1.38 
TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
        8.71        25.12        55.50        13.48         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49U 
       21.37        83.24        10.45        12.66         0.10        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
        0.10        13.25        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       22.39        15.52        11.54         4.47        25.25        10.52 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
        0.13         5.16        14.70        53.95        15.78         7.00 
TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
       20.02        20.38         5.29        15.35        19.96        18.31 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 
       30.71        15.06        15.91        10.16         3.42        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       19.56         9.47         6.61         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       17.29        39.12        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       12.16         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        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        3.45         9.07        12.76        17.49         0.69        12.26 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       20.55         0.56        12.95         2.66         2.20         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       11.80        19.17         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         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
        7.53         0.49        15.81         8.22        12.56        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        13.41        13.51         8.98        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         3.42 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        9.34         6.58         0.10        12.62         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-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 
       21.99         0.00         9.01        12.00        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 
        6.02         0.99       105.07        28.96        79.07        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        12.36        12.66        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       17.85        10.26        15.22        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        14.66        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
        7.99        16.24        14.47        21.27         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         5.52 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       18.08         5.92        14.27        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.76        24.30         5.59        12.30        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-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-A4H0 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RN 
        2.10         8.88         8.81        27.42         3.45        13.08 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 
        6.44        12.59        13.51         3.72        19.73         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         8.61         5.13        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87         5.46        35.24        21.73        27.88        32.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       28.96        34.29        16.31         2.50        12.79         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D 
        9.27        15.65        13.35        26.24        65.16        11.70 
TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A927 
       11.93        22.68         7.36         9.50         9.04         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-ZA-A8F6 
        5.72         2.66        28.41        26.04        10.62 

  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE 
                         12.935                          12.620 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (12.6)"
[1] "hr=" "1.1"
D92V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(21Q22.13) MUTATED         7        8       26       10        35
  DEL PEAK 53(21Q22.13) WILD-TYPE       4       11       22       22        42
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(21Q22.13) MUTATED          37        16         53         32
  DEL PEAK 53(21Q22.13) WILD-TYPE        47        13         44         40
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 53(21Q22.13) MUTATED           22       23         2
  DEL PEAK 53(21Q22.13) WILD-TYPE         26       28         2
D92V3, multiclass
            clus
vv           DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  STAGE I                                7                               4
  STAGE IA                               8                              11
  STAGE IB                              26                              22
  STAGE II                              10                              22
  STAGE IIA                             35                              42
  STAGE IIB                             37                              47
  STAGE III                             16                              13
  STAGE IIIA                            53                              44
  STAGE IIIB                            32                              40
  STAGE IIIC                            22                              26
  STAGE IV                              23                              28
  STAGE IVA                              2                               2
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 53(21Q22.13) MUTATED      24  60 139  52
  DEL PEAK 53(21Q22.13) WILD-TYPE    29  66 141  72
D92V4, multiclass
       clus
vv      DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  T0+T1                            24                              29
  T2                               60                              66
  T3                              139                             141
  T4                               52                              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 53(21Q22.13) MUTATED    92  89  46  46
  DEL PEAK 53(21Q22.13) WILD-TYPE 108  93  50  51
D92V5, multiclass
    clus
vv   DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  N0                            92                             108
  N1                            89                              93
  N2                            46                              50
  N3                            46                              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"
D92V6, binary
                                 cls
clus                                0   1
  DEL PEAK 53(21Q22.13) MUTATED   246  16
  DEL PEAK 53(21Q22.13) WILD-TYPE 267  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 53(21Q22.13) MUTATED    246   16
  DEL PEAK 53(21Q22.13) WILD-TYPE  267   23
   clus
vv  DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  0                           246                             267
  1                            16                              23
[1] 2 2
[1] FALSE
D92V7, binary
                                 cls
clus                                0   1
  DEL PEAK 53(21Q22.13) MUTATED    87 207
  DEL PEAK 53(21Q22.13) WILD-TYPE  95 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 53(21Q22.13) MUTATED     87  207
  DEL PEAK 53(21Q22.13) WILD-TYPE   95  220
        clus
vv       DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  FEMALE                            87                              95
  MALE                             207                             220
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 53(21Q22.13) MUTATED                                      26
  DEL PEAK 53(21Q22.13) WILD-TYPE                                    45
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(21Q22.13) MUTATED                                                       63
  DEL PEAK 53(21Q22.13) WILD-TYPE                                                     99
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(21Q22.13) MUTATED                                                                  42
  DEL PEAK 53(21Q22.13) WILD-TYPE                                                                39
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 53(21Q22.13) MUTATED                                                 41
  DEL PEAK 53(21Q22.13) WILD-TYPE                                               37
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 53(21Q22.13) MUTATED                                                         11
  DEL PEAK 53(21Q22.13) WILD-TYPE                                                       10
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 53(21Q22.13) MUTATED                                                           1
  DEL PEAK 53(21Q22.13) WILD-TYPE                                                         7
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 53(21Q22.13) MUTATED                                          8
  DEL PEAK 53(21Q22.13) WILD-TYPE                                        5
D92V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 53(21Q22.13) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      8
                                                                   clus
vv                                                                  DEL PEAK 53(21Q22.13) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                         99
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V9, binary
                                 cls
clus                                0   1
  DEL PEAK 53(21Q22.13) MUTATED     3 291
  DEL PEAK 53(21Q22.13) WILD-TYPE   3 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 53(21Q22.13) MUTATED      3  291
  DEL PEAK 53(21Q22.13) WILD-TYPE    3  312
     clus
vv    DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  NO                              3                               3
  YES                           291                             312
[1] 2 2
[1] FALSE
D92V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 53(21Q22.13) MUTATED   158   8   7   8
  DEL PEAK 53(21Q22.13) WILD-TYPE 189  10  12  17
D92V11, multiclass
    clus
vv   DEL PEAK 53(21Q22.13) MUTATED DEL PEAK 53(21Q22.13) WILD-TYPE
  R0                           158                             189
  R1                             8                              10
  R2                             7                              12
  RX                             8                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 53(21Q22.13) MUTATED      55                         8
  DEL PEAK 53(21Q22.13) WILD-TYPE    74                         5
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 53(21Q22.13) MUTATED                                           0
  DEL PEAK 53(21Q22.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 53(21Q22.13) MUTATED     188
  DEL PEAK 53(21Q22.13) WILD-TYPE   197
D92V13, multiclass
                                           clus
vv                                          DEL PEAK 53(21Q22.13) MUTATED
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               188
                                           clus
vv                                          DEL PEAK 53(21Q22.13) WILD-TYPE
  ASIAN                                                                  74
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V14, binary
                                 cls
clus                                0   1
  DEL PEAK 53(21Q22.13) MUTATED     4 168
  DEL PEAK 53(21Q22.13) WILD-TYPE   3 226
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 53(21Q22.13) MUTATED      4  168
  DEL PEAK 53(21Q22.13) WILD-TYPE    3  226
                        clus
vv                       DEL PEAK 53(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           168
                        clus
vv                       DEL PEAK 53(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             226
[1] 2 2
[1] FALSE

Clustering(93) Variable = DEL PEAK 54(22Q11.1) MUTATION ANALYSIS
D93V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 54(22Q11.1) MUTATED   123  91
  DEL PEAK 54(22Q11.1) WILD-TYPE 231 130
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                           214                            361 
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                            91                            130 
$`DEL PEAK 54(22Q11.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YB 
       13.94         8.94        16.24         4.21        32.45         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-JY-A6F8 
       18.64         3.88         0.53         0.79        23.41       122.10 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A4OE TCGA-L5-A4OG 
       42.77        25.41        31.56         3.16        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61        18.35         7.17         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 
       29.00         7.13         2.60         0.36         7.40         3.95 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.02        55.50         2.66        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.55        13.22         5.49         8.71        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W 
        5.92        10.45        13.41         0.10        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN 
        0.10        12.76        10.52        12.03        13.18         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.59         5.06        15.78         2.89         1.45         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EU 
        5.29         4.80         9.27        18.81        22.82        18.31 
TCGA-VR-A8EZ TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
       18.18         2.10         2.66        19.73        11.01         9.44 
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 
        6.61        17.29        19.33        26.10         9.17        12.16 
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8058 TCGA-BR-8059 
        9.21        15.42        28.01        28.73        17.49        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 
       11.44         9.60         7.40        14.04        25.18         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ 
       11.54        16.44         8.22        10.68        13.87        22.26 
TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 
        0.72        19.36        20.65         1.15        13.64        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 
        0.30         0.07         0.07         0.07         0.16         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        3.42        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 
        3.02         8.05        54.08         4.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 
       19.07        21.99        18.97        30.97        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       69.04        12.66        11.93        20.55        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 
       15.22        12.79        11.31        19.50        18.21        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO 
       16.44        11.31        15.65         7.40         0.62        16.24 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-8604 
       19.53        17.06         0.56         5.52        14.17        12.10 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       12.30         9.67        27.42         3.39        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU 
       13.08         1.41         6.44         6.74        12.59         1.81 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G TCGA-MX-A663 TCGA-R5-A7O7 
        7.82         2.53         5.56        20.15         9.86        45.67 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N1 
        6.08         9.24         8.61         5.13        16.67       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       18.48        46.26        22.19        12.79        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       27.35        14.33        36.69        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T 
       36.16         9.50         9.73         4.54        64.18        11.24 
TCGA-VQ-A94U TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       22.09        32.94        29.98         0.79 

$`DEL PEAK 54(22Q11.1) WILD-TYPE`
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.69         6.21        33.27        20.09         0.85        20.78 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
       20.12         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD 
        4.67        14.50        12.16        44.75        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        23.18        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF 
        6.28        30.25         0.30         4.31         8.94         3.68 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OX 
       19.99        21.01        47.93         3.32         1.38         7.43 
TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ 
        6.94         8.71        25.12        35.97         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N 
       13.41        27.12        83.24        52.57        12.66        12.43 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.15         0.10        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO 
        4.47        12.33        25.25        12.00        12.23         0.13 
TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         5.16         7.82        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW 
        6.35        53.95         9.30        12.69        20.02        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35         4.44        19.96        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        28.11        30.71        42.87        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 
       11.24         9.17        15.91        10.16         3.42        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.70        19.56         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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-6566 TCGA-BR-6705 
       15.95        13.87        13.68        39.12        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82        24.76        35.24        23.93        18.15 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        12.43         3.45         9.07        12.76        18.71 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        2.66        16.31         2.20        15.58         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        19.17        14.79         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       15.85         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       15.81         9.86        15.68        12.56         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        13.51         0.46        20.42 
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-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
        0.10         9.34         6.58         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
       15.95         1.02         7.99        14.01        12.03         0.00 
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        36.00 
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-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10         4.01        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       15.98        10.55        12.33        24.72        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        8.38         4.34         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       21.27        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03        13.58         0.23        18.08        26.47         1.51 
TCGA-HU-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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        6.51        10.19        19.36         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
        3.45        18.81         5.19         6.51         5.56        13.51 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF 
       60.56        37.64         3.72        19.73        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       61.25         4.60        11.05       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        35.24        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
        7.73        28.96        34.29        16.31         2.50         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       65.16        11.70        11.93        61.22        22.68         7.36 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       52.24         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        40.08        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                         122.1                          122.3 
  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE 
                        12.365                         12.820 
[1] "0.1 - 122.1 (12.4)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D93V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 54(22Q11.1) MUTATED         6        6       19       12        23
  DEL PEAK 54(22Q11.1) WILD-TYPE       5       13       29       20        54
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 54(22Q11.1) MUTATED          28        19         36         27
  DEL PEAK 54(22Q11.1) WILD-TYPE        56        10         61         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 54(22Q11.1) MUTATED           14       16         3
  DEL PEAK 54(22Q11.1) WILD-TYPE         34       35         1
D93V3, multiclass
            clus
vv           DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  STAGE I                               6                              5
  STAGE IA                              6                             13
  STAGE IB                             19                             29
  STAGE II                             12                             20
  STAGE IIA                            23                             54
  STAGE IIB                            28                             56
  STAGE III                            19                             10
  STAGE IIIA                           36                             61
  STAGE IIIB                           27                             45
  STAGE IIIC                           14                             34
  STAGE IV                             16                             35
  STAGE IVA                             3                              1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 54(22Q11.1) MUTATED      26  40 118  30
  DEL PEAK 54(22Q11.1) WILD-TYPE    27  86 162  94
D93V4, multiclass
       clus
vv      DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  T0+T1                           26                             27
  T2                              40                             86
  T3                             118                            162
  T4                              30                             94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 54(22Q11.1) MUTATED    68  69  36  36
  DEL PEAK 54(22Q11.1) WILD-TYPE 132 113  60  61
D93V5, multiclass
    clus
vv   DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  N0                           68                            132
  N1                           69                            113
  N2                           36                             60
  N3                           36                             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"
D93V6, binary
                                cls
clus                               0   1
  DEL PEAK 54(22Q11.1) MUTATED   188  13
  DEL PEAK 54(22Q11.1) WILD-TYPE 325  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(22Q11.1) MUTATED    188   13
  DEL PEAK 54(22Q11.1) WILD-TYPE  325   26
   clus
vv  DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  0                          188                            325
  1                           13                             26
[1] 2 2
[1] FALSE
D93V7, binary
                                cls
clus                               0   1
  DEL PEAK 54(22Q11.1) MUTATED    61 163
  DEL PEAK 54(22Q11.1) WILD-TYPE 121 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(22Q11.1) MUTATED     61  163
  DEL PEAK 54(22Q11.1) WILD-TYPE  121  264
        clus
vv       DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  FEMALE                           61                            121
  MALE                            163                            264
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 54(22Q11.1) MUTATED                                      17
  DEL PEAK 54(22Q11.1) WILD-TYPE                                    54
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 54(22Q11.1) MUTATED                                                       58
  DEL PEAK 54(22Q11.1) WILD-TYPE                                                    104
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 54(22Q11.1) MUTATED                                                                  25
  DEL PEAK 54(22Q11.1) WILD-TYPE                                                                56
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 54(22Q11.1) MUTATED                                                 31
  DEL PEAK 54(22Q11.1) WILD-TYPE                                               47
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 54(22Q11.1) MUTATED                                                          8
  DEL PEAK 54(22Q11.1) WILD-TYPE                                                       13
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 54(22Q11.1) MUTATED                                                           3
  DEL PEAK 54(22Q11.1) WILD-TYPE                                                         5
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 54(22Q11.1) MUTATED                                          6
  DEL PEAK 54(22Q11.1) WILD-TYPE                                        7
D93V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 54(22Q11.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      58
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     6
                                                                   clus
vv                                                                  DEL PEAK 54(22Q11.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                       7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V9, binary
                                cls
clus                               0   1
  DEL PEAK 54(22Q11.1) MUTATED     3 221
  DEL PEAK 54(22Q11.1) WILD-TYPE   3 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(22Q11.1) MUTATED      3  221
  DEL PEAK 54(22Q11.1) WILD-TYPE    3  382
     clus
vv    DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  NO                             3                              3
  YES                          221                            382
[1] 2 2
[1] FALSE
D93V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 54(22Q11.1) MUTATED   114   7   9   7
  DEL PEAK 54(22Q11.1) WILD-TYPE 233  11  10  18
D93V11, multiclass
    clus
vv   DEL PEAK 54(22Q11.1) MUTATED DEL PEAK 54(22Q11.1) WILD-TYPE
  R0                          114                            233
  R1                            7                             11
  R2                            9                             10
  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"
D93V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 54(22Q11.1) MUTATED      42                         3
  DEL PEAK 54(22Q11.1) WILD-TYPE    87                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 54(22Q11.1) MUTATED                                           1
  DEL PEAK 54(22Q11.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 54(22Q11.1) MUTATED     142
  DEL PEAK 54(22Q11.1) WILD-TYPE   243
D93V13, multiclass
                                           clus
vv                                          DEL PEAK 54(22Q11.1) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              142
                                           clus
vv                                          DEL PEAK 54(22Q11.1) WILD-TYPE
  ASIAN                                                                 87
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V14, binary
                                cls
clus                               0   1
  DEL PEAK 54(22Q11.1) MUTATED     2 133
  DEL PEAK 54(22Q11.1) WILD-TYPE   5 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 54(22Q11.1) MUTATED      2  133
  DEL PEAK 54(22Q11.1) WILD-TYPE    5  261
                        clus
vv                       DEL PEAK 54(22Q11.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 54(22Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(94) Variable = DEL PEAK 55(22Q13.31) MUTATION ANALYSIS
D94V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 55(22Q13.31) MUTATED   125  95
  DEL PEAK 55(22Q13.31) WILD-TYPE 229 126
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                            220                             355 
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                             95                             126 
$`DEL PEAK 55(22Q13.31) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       25.78        31.27        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        18.64         3.88         0.53         0.79        23.41 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93D TCGA-L5-A4OE 
        4.67       122.10        42.77        25.41        31.56        24.00 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        4.70        32.61         1.38        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.13         7.40         3.02         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NW 
       16.47        13.55        13.22         5.49         8.71        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U 
       10.36         5.92        10.45        13.41         0.10        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HY 
       13.25         0.10        12.76        11.54        10.52        12.03 
TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 
       13.18         8.02         7.59         5.06        29.59        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
       15.78         2.89         7.00         5.29         4.80         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EY TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.81        19.96        22.82        30.71         2.10         2.66 
TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 
       19.73        11.01         9.44         6.61        18.35         6.18 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 
       17.29        19.33        26.10         9.17        12.16         9.21 
TCGA-BR-7715 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       15.42        17.49        14.43        11.44         0.69         9.60 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 
        2.20         7.40         6.18        19.50        14.04        25.18 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        16.44         9.86         8.22        10.68 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
       22.26        12.89         0.72        19.36        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 
       13.64         3.25        13.15         0.07         0.07         0.16 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         3.42         9.34        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       12.20         3.02         8.05        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 
       47.05        19.07        21.99        18.97        30.97        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 
       15.02        69.04        12.66        11.93        20.55        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        15.22        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       24.72        19.50        18.21        21.14        16.44        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8099 
       15.65         7.40         0.62        16.24        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP 
        0.56         5.52         5.92        14.17        22.75         8.98 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        0.26         2.10        12.95        23.84         9.67        27.42 
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-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93G 
        6.74         1.81         7.82         2.53         5.56        20.15 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 
        9.86        45.67        18.21         6.08         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
      115.69        35.61         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PC 
       13.25        13.02        18.48        35.24        32.48        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY 
       22.19        12.79        17.85         1.87        27.35        14.33 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       36.69        18.74        20.81         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U 
        9.73         9.04         4.54        64.18        11.24        22.09 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       18.41        32.94        29.98         0.79 

$`DEL PEAK 55(22Q13.31) WILD-TYPE`
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        7.69         6.21        20.09         0.85        20.78        20.12 
TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        9.30        17.03        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16        44.75        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        23.18        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OI 
       30.25         0.30         4.31         8.94         3.68        19.99 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         7.17         3.16 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y 
        7.43         6.94         8.71         2.60        25.12         0.36 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
        3.95        55.50        35.97         7.76        21.37        13.41 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S 
       27.12        83.24        52.57        12.66        12.43        13.15 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
        0.10        12.46        12.59        12.49        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
        0.10        15.52        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU 
       25.25        12.00        12.23         0.13        33.11         5.16 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC 
        7.82        14.70         7.04         6.35         9.30         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
       12.69        20.02        20.38         3.42        15.35         4.44 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       12.43         1.55        18.31         8.12        28.11        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       42.87        46.19        15.06        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       10.16         3.42        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 
        6.97         4.64         7.43        30.90         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 
       34.68        15.95        13.87        13.68        39.12        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94        12.82        24.76        35.24        23.93 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        9.07        12.76        18.71        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 
        0.56        12.95         2.66        16.31        15.58        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        19.17        14.79         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         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         9.34        13.45         6.28         7.53        15.81 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       15.68        12.56        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         8.98        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
        0.66        13.51         0.46        20.42        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 
        2.83        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        6.58         0.10        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        1.02         7.99        29.98        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-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-D7-6518 
       65.10         4.01        21.07         7.99        12.36        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 
       18.84        18.54        18.61        17.85        15.98        10.55 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        17.19        14.66        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
        9.76         2.96         8.38         4.34         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
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-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        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-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 
        0.10         6.51         6.25        10.19        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RO 
        8.88         8.81        21.21         3.45        18.81         1.41 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H 
       12.59         6.51         5.56        13.51        60.56        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73         8.52        61.25         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         5.13       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E3 
       71.38        57.44         8.94        16.87        19.04        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       34.45        27.88         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.50         2.70         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       26.24        64.57        65.16        11.70        11.93        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       22.68         7.36        52.24         2.01        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        21.04         2.66        42.54        40.08        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        21.11        12.43 
TCGA-ZA-A8F6 
       10.62 

  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                          122.1                           122.3 
  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE 
                         12.775                          12.760 
[1] "0.1 - 122.1 (12.8)" "0.0 - 122.3 (12.8)"
[1] "hr=" "1.3"
D94V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 55(22Q13.31) MUTATED         6        1       19       11        27
  DEL PEAK 55(22Q13.31) WILD-TYPE       5       18       29       21        50
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 55(22Q13.31) MUTATED          28        18         42         30
  DEL PEAK 55(22Q13.31) WILD-TYPE        56        11         55         42
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 55(22Q13.31) MUTATED           16       17         3
  DEL PEAK 55(22Q13.31) WILD-TYPE         32       34         1
D94V3, multiclass
            clus
vv           DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  STAGE I                                6                               5
  STAGE IA                               1                              18
  STAGE IB                              19                              29
  STAGE II                              11                              21
  STAGE IIA                             27                              50
  STAGE IIB                             28                              56
  STAGE III                             18                              11
  STAGE IIIA                            42                              55
  STAGE IIIB                            30                              42
  STAGE IIIC                            16                              32
  STAGE IV                              17                              34
  STAGE IVA                              3                               1
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 55(22Q13.31) MUTATED      18  45 118  39
  DEL PEAK 55(22Q13.31) WILD-TYPE    35  81 162  85
D94V4, multiclass
       clus
vv      DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  T0+T1                            18                              35
  T2                               45                              81
  T3                              118                             162
  T4                               39                              85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 55(22Q13.31) MUTATED    67  69  44  37
  DEL PEAK 55(22Q13.31) WILD-TYPE 133 113  52  60
D94V5, multiclass
    clus
vv   DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  N0                            67                             133
  N1                            69                             113
  N2                            44                              52
  N3                            37                              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"
D94V6, binary
                                 cls
clus                                0   1
  DEL PEAK 55(22Q13.31) MUTATED   201  12
  DEL PEAK 55(22Q13.31) WILD-TYPE 312  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 55(22Q13.31) MUTATED    201   12
  DEL PEAK 55(22Q13.31) WILD-TYPE  312   27
   clus
vv  DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  0                           201                             312
  1                            12                              27
[1] 2 2
[1] FALSE
D94V7, binary
                                 cls
clus                                0   1
  DEL PEAK 55(22Q13.31) MUTATED    64 167
  DEL PEAK 55(22Q13.31) WILD-TYPE 118 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 55(22Q13.31) MUTATED     64  167
  DEL PEAK 55(22Q13.31) WILD-TYPE  118  260
        clus
vv       DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  FEMALE                            64                             118
  MALE                             167                             260
[1] 2 2
[1] FALSE
                                 vv
clus                              STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 55(22Q13.31) MUTATED                                      18
  DEL PEAK 55(22Q13.31) WILD-TYPE                                    53
                                 vv
clus                              STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 55(22Q13.31) MUTATED                                                       56
  DEL PEAK 55(22Q13.31) WILD-TYPE                                                    106
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 55(22Q13.31) MUTATED                                                                  27
  DEL PEAK 55(22Q13.31) WILD-TYPE                                                                54
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 55(22Q13.31) MUTATED                                                 40
  DEL PEAK 55(22Q13.31) WILD-TYPE                                               38
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 55(22Q13.31) MUTATED                                                          9
  DEL PEAK 55(22Q13.31) WILD-TYPE                                                       12
                                 vv
clus                              STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 55(22Q13.31) MUTATED                                                           2
  DEL PEAK 55(22Q13.31) WILD-TYPE                                                         6
                                 vv
clus                              STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 55(22Q13.31) MUTATED                                          6
  DEL PEAK 55(22Q13.31) WILD-TYPE                                        7
D94V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 55(22Q13.31) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       56
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      6
                                                                   clus
vv                                                                  DEL PEAK 55(22Q13.31) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                          53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                        106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                              54
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                               38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                       12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                        7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V9, binary
                                 cls
clus                                0   1
  DEL PEAK 55(22Q13.31) MUTATED     4 227
  DEL PEAK 55(22Q13.31) WILD-TYPE   2 376
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 55(22Q13.31) MUTATED      4  227
  DEL PEAK 55(22Q13.31) WILD-TYPE    2  376
     clus
vv    DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  NO                              4                               2
  YES                           227                             376
[1] 2 2
[1] FALSE
D94V10, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 55(22Q13.31) MUTATED   122   8   9   8
  DEL PEAK 55(22Q13.31) WILD-TYPE 225  10  10  17
D94V11, multiclass
    clus
vv   DEL PEAK 55(22Q13.31) MUTATED DEL PEAK 55(22Q13.31) WILD-TYPE
  R0                           122                             225
  R1                             8                              10
  R2                             9                              10
  RX                             8                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 55(22Q13.31) MUTATED      45                         3
  DEL PEAK 55(22Q13.31) WILD-TYPE    84                        10
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 55(22Q13.31) MUTATED                                           1
  DEL PEAK 55(22Q13.31) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 55(22Q13.31) MUTATED     144
  DEL PEAK 55(22Q13.31) WILD-TYPE   241
D94V13, multiclass
                                           clus
vv                                          DEL PEAK 55(22Q13.31) MUTATED
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               144
                                           clus
vv                                          DEL PEAK 55(22Q13.31) WILD-TYPE
  ASIAN                                                                  84
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V14, binary
                                 cls
clus                                0   1
  DEL PEAK 55(22Q13.31) MUTATED     2 141
  DEL PEAK 55(22Q13.31) WILD-TYPE   5 253
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 55(22Q13.31) MUTATED      2  141
  DEL PEAK 55(22Q13.31) WILD-TYPE    5  253
                        clus
vv                       DEL PEAK 55(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           141
                        clus
vv                       DEL PEAK 55(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             253
[1] 2 2
[1] FALSE

Clustering(95) Variable = DEL PEAK 56(XP22.2) MUTATION ANALYSIS
D95V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 56(XP22.2) MUTATED    90  48
  DEL PEAK 56(XP22.2) WILD-TYPE 264 173
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                          138                           437 
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                           48                           173 
$`DEL PEAK 56(XP22.2) MUTATED`
TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       14.30         4.21        32.45        33.27        20.09        20.78 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         0.53        17.03        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A4OE 
        4.67        44.75        42.77        25.41        23.18        24.00 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ 
        3.68        21.01        18.35         7.17         3.95        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        8.71        13.41        46.09         5.92        10.45        12.66 
TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 
        0.10         0.10        12.46        12.59        12.49        22.39 
TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ 
       13.22        12.33        25.25        10.52        12.00        13.18 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV 
        0.13        33.11        15.78         1.45        12.69        20.02 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ 
        9.27         4.44        18.81        18.31         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TN 
       42.87        15.91        10.16         3.42         2.10         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8289 TCGA-BR-8297 
       18.35        19.33        28.01        14.43         2.66         7.40 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8680 
       13.08        14.04         9.21        20.22         9.34        15.81 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD 
        9.86        10.68        13.87        22.26         0.66        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8531 
        1.15        13.64         3.25         0.30         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4438 
        0.13         0.13         9.34        11.31        12.20        54.08 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5725 
       14.01        47.05        19.07        21.99        36.00        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        7.99        11.93        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.79        12.33        18.21        11.31         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4G3 
       15.65         7.40         0.62        13.58         5.52         5.59 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 
       22.75        25.81         6.25        12.30        21.21         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-R5-A7O7 TCGA-RD-A8N6 
        3.39        18.38         5.19         6.44        45.67         8.94 
TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Y 
       32.48        46.26         1.87        13.35        27.35         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A 
       52.24         9.04         5.72        22.09        40.08        32.94 

$`DEL PEAK 56(XP22.2) WILD-TYPE`
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94        16.24         7.69         6.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H 
       20.12        18.64         9.30         0.79        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       12.16       122.10        60.39        68.02         3.68        41.52 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       21.70        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH 
       30.25         0.30         4.31         8.94         4.70        32.61 
TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       19.99        47.93         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         0.36         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.36        12.43        13.41        13.15        15.35         0.10 
TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.25        12.76        12.59         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FU TCGA-Q9-A6FW 
       12.33         4.47        12.23        12.03         5.16         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
        6.35        53.95         9.30         2.89         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
        5.29         3.42         4.80        15.35        19.96        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G 
       12.43         1.55        28.11        30.71        46.19        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       11.24         9.17         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       15.32        28.73        12.43         3.45         9.07        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49        11.44         0.69        12.26         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         8.05         0.56        12.95        16.31         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       15.58         6.18        19.50         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        19.17 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         0.26        15.85         3.72         5.39        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        15.81        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        0.49        11.54        16.44        15.68         8.22        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
        8.98         0.72        14.17         0.53        12.82        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46        20.42        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.16         0.10         0.10         3.42 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58         0.10        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        29.98        12.03         0.00         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        69.04        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        14.66        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 
       11.24        11.44         8.38         4.34         7.13         7.99 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76        24.30        12.30        11.84        24.20         3.25 
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        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ 
        9.67         8.88         8.81        27.42        18.81         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.08         1.41         6.74        12.59         6.51         5.56 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.81         7.82        13.51         2.53         5.56        60.56 
TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE 
       20.15        37.64         3.72        19.73         9.86        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        61.25         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       19.04         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        35.24        21.73        34.45        27.88 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        28.96        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70        17.85         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       26.24        64.57        14.33        65.16        36.69        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.93        61.22        18.74        20.81        22.68         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       36.16         7.36         9.50         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58        64.18        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        29.98        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE 
                        12.74                         12.76 
[1] "0.1 - 54.1 (12.7)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D95V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 56(XP22.2) MUTATED         2        2        7        8        24
  DEL PEAK 56(XP22.2) WILD-TYPE       9       17       41       24        53
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 56(XP22.2) MUTATED          26         8         26         12
  DEL PEAK 56(XP22.2) WILD-TYPE        58        21         71         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 56(XP22.2) MUTATED            9       10         1
  DEL PEAK 56(XP22.2) WILD-TYPE         39       41         3
D95V3, multiclass
            clus
vv           DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             2                            17
  STAGE IB                             7                            41
  STAGE II                             8                            24
  STAGE IIA                           24                            53
  STAGE IIB                           26                            58
  STAGE III                            8                            21
  STAGE IIIA                          26                            71
  STAGE IIIB                          12                            60
  STAGE IIIC                           9                            39
  STAGE IV                            10                            41
  STAGE IVA                            1                             3
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 56(XP22.2) MUTATED      10  34  69  25
  DEL PEAK 56(XP22.2) WILD-TYPE    43  92 211  99
D95V4, multiclass
       clus
vv      DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  T0+T1                          10                            43
  T2                             34                            92
  T3                             69                           211
  T4                             25                            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 56(XP22.2) MUTATED    48  48  24  17
  DEL PEAK 56(XP22.2) WILD-TYPE 152 134  72  80
D95V5, multiclass
    clus
vv   DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  N0                          48                           152
  N1                          48                           134
  N2                          24                            72
  N3                          17                            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"
D95V6, binary
                               cls
clus                              0   1
  DEL PEAK 56(XP22.2) MUTATED   124   8
  DEL PEAK 56(XP22.2) WILD-TYPE 389  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 56(XP22.2) MUTATED    124    8
  DEL PEAK 56(XP22.2) WILD-TYPE  389   31
   clus
vv  DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  0                         124                           389
  1                           8                            31
[1] 2 2
[1] FALSE
D95V7, binary
                               cls
clus                              0   1
  DEL PEAK 56(XP22.2) MUTATED    30 113
  DEL PEAK 56(XP22.2) WILD-TYPE 152 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 56(XP22.2) MUTATED     30  113
  DEL PEAK 56(XP22.2) WILD-TYPE  152  314
        clus
vv       DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  FEMALE                          30                           152
  MALE                           113                           314
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 56(XP22.2) MUTATED                                       9
  DEL PEAK 56(XP22.2) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 56(XP22.2) MUTATED                                                       29
  DEL PEAK 56(XP22.2) WILD-TYPE                                                    133
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 56(XP22.2) MUTATED                                                                  14
  DEL PEAK 56(XP22.2) WILD-TYPE                                                                67
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 56(XP22.2) MUTATED                                                 21
  DEL PEAK 56(XP22.2) WILD-TYPE                                               57
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 56(XP22.2) MUTATED                                                          2
  DEL PEAK 56(XP22.2) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 56(XP22.2) MUTATED                                                           3
  DEL PEAK 56(XP22.2) WILD-TYPE                                                         5
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 56(XP22.2) MUTATED                                          4
  DEL PEAK 56(XP22.2) WILD-TYPE                                        9
D95V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 56(XP22.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 56(XP22.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V9, binary
                               cls
clus                              0   1
  DEL PEAK 56(XP22.2) MUTATED     1 142
  DEL PEAK 56(XP22.2) WILD-TYPE   5 461
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 56(XP22.2) MUTATED      1  142
  DEL PEAK 56(XP22.2) WILD-TYPE    5  461
     clus
vv    DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  NO                            1                             5
  YES                         142                           461
[1] 2 2
[1] FALSE
D95V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 56(XP22.2) MUTATED    67   3   3   2
  DEL PEAK 56(XP22.2) WILD-TYPE 280  15  16  23
D95V11, multiclass
    clus
vv   DEL PEAK 56(XP22.2) MUTATED DEL PEAK 56(XP22.2) WILD-TYPE
  R0                          67                           280
  R1                           3                            15
  R2                           3                            16
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 56(XP22.2) MUTATED      41                         0
  DEL PEAK 56(XP22.2) WILD-TYPE    88                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 56(XP22.2) MUTATED                                           0    88
  DEL PEAK 56(XP22.2) WILD-TYPE                                         1   297
D95V13, multiclass
                                           clus
vv                                          DEL PEAK 56(XP22.2) MUTATED
  ASIAN                                                              41
  BLACK OR AFRICAN AMERICAN                                           0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              88
                                           clus
vv                                          DEL PEAK 56(XP22.2) WILD-TYPE
  ASIAN                                                                88
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               297
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V14, binary
                               cls
clus                              0   1
  DEL PEAK 56(XP22.2) MUTATED     2  97
  DEL PEAK 56(XP22.2) WILD-TYPE   5 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 56(XP22.2) MUTATED      2   97
  DEL PEAK 56(XP22.2) WILD-TYPE    5  297
                        clus
vv                       DEL PEAK 56(XP22.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK 56(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           297
[1] 2 2
[1] FALSE

Clustering(96) Variable = DEL PEAK 57(XP21.1) MUTATION ANALYSIS
D96V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 57(XP21.1) MUTATED    79  53
  DEL PEAK 57(XP21.1) WILD-TYPE 275 168
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                          132                           443 
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                           53                           168 
$`DEL PEAK 57(XP21.1) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78        14.30         4.21        32.45        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
        0.85        20.78         3.88         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A938 
       12.82         9.96         4.67        44.75        42.77        25.41 
TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       23.18         4.31        24.00         3.68        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NS 
       18.35         7.17         1.38         3.95        16.47        13.41 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
        5.92        12.66         0.10        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       22.39        13.22        12.33        25.25        10.52        12.00 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A8W8 
       13.18         0.13        33.11         5.16         8.02         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX 
        1.45        12.69        20.02         5.29         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I 
       18.81        18.31         8.12        18.18        42.87        15.91 
TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
       10.16         3.42         2.10        19.56         9.44        18.35 
TCGA-BR-6458 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 
       19.33        14.43        16.31         7.40        13.08        17.52 
TCGA-BR-8369 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J6 
       14.04         9.86        13.87         7.53        22.26         0.66 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8533 TCGA-CD-A489 
       20.65         1.15        13.64         0.07         0.13        11.31 
TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       12.20         8.05        54.08        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 
       21.99         7.07        15.02         7.99        11.93        19.13 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 
       13.35        15.22        15.98        12.79        12.33        18.21 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 
       11.31         9.76        15.65         7.40         0.62        13.58 
TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        5.52        22.75        12.30         3.45         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A8N6 TCGA-VQ-A8PC 
        5.19         6.44        37.64        45.67         8.94        46.26 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 
       13.35        27.35        14.33        18.74        52.24         9.04 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       22.09        18.41        40.08        32.94        17.13        21.11 

$`DEL PEAK 57(XP21.1) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        58.55         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         7.69         6.21         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.30         0.79        14.86        14.50        12.16       122.10 
TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       60.39        68.02         3.68        41.52        21.70        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       25.22        24.03         6.28         3.16        30.25         0.30 
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OR 
        8.94         4.70        32.61        19.99         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       58.59         4.90        29.00         7.13         7.43         6.94 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 
        8.71         2.60        25.12         0.36         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       55.50         2.66        35.97        12.92        13.48        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NT 
       13.22         7.76         5.49        21.37         8.71        27.12 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N 
       83.24        52.57        46.09        10.36        10.45        12.43 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59         0.10        15.52        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
        4.47        12.23        12.03         7.82         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       15.78         7.00        20.38         3.42         4.80        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        22.82        12.43         1.55        28.11        30.71 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19        15.06        11.24         9.17         2.66        19.73 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.64         7.43        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01        18.15        15.32        28.73        12.43         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        9.07        12.76        18.71        17.49        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         9.60        20.55         8.05         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66         2.20        15.58         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        13.45         6.28         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44        15.68         8.22        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        13.41        13.51        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         3.42         9.34        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58         0.10        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
       15.95         1.02         7.99         4.01        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.00         9.01        18.97        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
       69.04        21.07        12.36        12.66        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 
       18.54        18.61        17.85        17.19        10.26        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       11.31        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        13.71        11.24        11.44         2.96 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
        8.38         4.34         7.13         7.99        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A8CX 
       22.29        17.06        59.54         5.03         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         5.36        13.08         1.41         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51         5.56         1.81         7.82        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        20.15         3.72        19.73         9.86 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        61.25         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       27.88        32.48         7.73        28.96        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        26.24        64.57        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       36.69        11.70        11.93        61.22        20.81        22.68 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        36.16         7.36         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        64.18        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        2.66        42.54        11.24        28.41        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        10.62         0.79 

  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                        54.08                        122.30 
  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE 
                        13.35                         12.59 
[1] "0.1 - 54.1 (13.3)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1.1"
D96V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 57(XP21.1) MUTATED         2        3        5        5        21
  DEL PEAK 57(XP21.1) WILD-TYPE       9       16       43       27        56
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 57(XP21.1) MUTATED          24         8         27         15
  DEL PEAK 57(XP21.1) WILD-TYPE        60        21         70         57
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 57(XP21.1) MUTATED            7        8         0
  DEL PEAK 57(XP21.1) WILD-TYPE         41       43         4
D96V3, multiclass
            clus
vv           DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             3                            16
  STAGE IB                             5                            43
  STAGE II                             5                            27
  STAGE IIA                           21                            56
  STAGE IIB                           24                            60
  STAGE III                            8                            21
  STAGE IIIA                          27                            70
  STAGE IIIB                          15                            57
  STAGE IIIC                           7                            41
  STAGE IV                             8                            43
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 57(XP21.1) MUTATED      12  30  63  24
  DEL PEAK 57(XP21.1) WILD-TYPE    41  96 217 100
D96V4, multiclass
       clus
vv      DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  T0+T1                          12                            41
  T2                             30                            96
  T3                             63                           217
  T4                             24                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 57(XP21.1) MUTATED    46  42  25  15
  DEL PEAK 57(XP21.1) WILD-TYPE 154 140  71  82
D96V5, multiclass
    clus
vv   DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  N0                          46                           154
  N1                          42                           140
  N2                          25                            71
  N3                          15                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V6, binary
                               cls
clus                              0   1
  DEL PEAK 57(XP21.1) MUTATED   114   5
  DEL PEAK 57(XP21.1) WILD-TYPE 399  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 57(XP21.1) MUTATED    114    5
  DEL PEAK 57(XP21.1) WILD-TYPE  399   34
   clus
vv  DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  0                         114                           399
  1                           5                            34
[1] 2 2
[1] FALSE
D96V7, binary
                               cls
clus                              0   1
  DEL PEAK 57(XP21.1) MUTATED    28 108
  DEL PEAK 57(XP21.1) WILD-TYPE 154 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 57(XP21.1) MUTATED     28  108
  DEL PEAK 57(XP21.1) WILD-TYPE  154  319
        clus
vv       DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  FEMALE                          28                           154
  MALE                           108                           319
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 57(XP21.1) MUTATED                                       9
  DEL PEAK 57(XP21.1) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 57(XP21.1) MUTATED                                                       22
  DEL PEAK 57(XP21.1) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 57(XP21.1) MUTATED                                                                  14
  DEL PEAK 57(XP21.1) WILD-TYPE                                                                67
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 57(XP21.1) MUTATED                                                 20
  DEL PEAK 57(XP21.1) WILD-TYPE                                               58
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 57(XP21.1) MUTATED                                                          2
  DEL PEAK 57(XP21.1) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 57(XP21.1) MUTATED                                                           1
  DEL PEAK 57(XP21.1) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 57(XP21.1) MUTATED                                          3
  DEL PEAK 57(XP21.1) WILD-TYPE                                       10
D96V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 57(XP21.1) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 57(XP21.1) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V9, binary
                               cls
clus                              0   1
  DEL PEAK 57(XP21.1) MUTATED     1 135
  DEL PEAK 57(XP21.1) WILD-TYPE   5 468
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 57(XP21.1) MUTATED      1  135
  DEL PEAK 57(XP21.1) WILD-TYPE    5  468
     clus
vv    DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  NO                            1                             5
  YES                         135                           468
[1] 2 2
[1] FALSE
D96V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 57(XP21.1) MUTATED    56   5   2   2
  DEL PEAK 57(XP21.1) WILD-TYPE 291  13  17  23
D96V11, multiclass
    clus
vv   DEL PEAK 57(XP21.1) MUTATED DEL PEAK 57(XP21.1) WILD-TYPE
  R0                          56                           291
  R1                           5                            13
  R2                           2                            17
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 57(XP21.1) MUTATED      32                         1
  DEL PEAK 57(XP21.1) WILD-TYPE    97                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 57(XP21.1) MUTATED                                           0    85
  DEL PEAK 57(XP21.1) WILD-TYPE                                         1   300
D96V13, multiclass
                                           clus
vv                                          DEL PEAK 57(XP21.1) MUTATED
  ASIAN                                                              32
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              85
                                           clus
vv                                          DEL PEAK 57(XP21.1) WILD-TYPE
  ASIAN                                                                97
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               300
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V14, binary
                               cls
clus                              0   1
  DEL PEAK 57(XP21.1) MUTATED     3  84
  DEL PEAK 57(XP21.1) WILD-TYPE   4 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 57(XP21.1) MUTATED      3   84
  DEL PEAK 57(XP21.1) WILD-TYPE    4  310
                        clus
vv                       DEL PEAK 57(XP21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       DEL PEAK 57(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           310
[1] 2 2
[1] FALSE

Clustering(97) Variable = DEL PEAK 58(XP11.3) MUTATION ANALYSIS
D97V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 58(XP11.3) MUTATED    83  51
  DEL PEAK 58(XP11.3) WILD-TYPE 271 170
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                          134                           441 
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                           51                           170 
$`DEL PEAK 58(XP11.3) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL 
       25.78        14.30         8.94         4.21        32.45        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12         3.88         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.79        23.41        12.82         9.96         4.67        44.75 
TCGA-JY-A6FH TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF 
       42.77        25.41        23.18         4.31        24.00         3.68 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ 
       21.01        47.93        18.35         7.17         3.95        16.47 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49W 
        8.71        13.41         5.92        12.66         0.10        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 
        0.10        12.46        12.59        12.49        22.39        11.54 
TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       13.22        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-Q9-A6FU TCGA-R6-A8W8 TCGA-R6-A8WC 
       13.18         0.13        33.11         5.16         2.89         1.45 
TCGA-R6-A8WG TCGA-S8-A6BV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69        20.02         9.27         4.44        18.81        19.96 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD 
       18.31         8.12        42.87        15.91        10.16         3.42 
TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8059 
        2.10        19.56         9.44        18.35        19.33        14.43 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8485 TCGA-BR-8683 
       16.31         7.40        13.08        17.52         9.21         9.86 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8533 TCGA-CD-A489 
       13.87        22.26        13.64         0.07         0.13        11.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4444 
       12.43        12.20         3.02         8.05        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 TCGA-D7-5579 
       19.07        21.99         7.07        15.02         7.99        11.93 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 
       13.35        15.22        15.98        12.79        12.33        18.21 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8211 
       11.31         9.76         7.40         0.62         7.99        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-A4GD TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        5.52         0.23        22.75        12.95        23.84        12.30 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP 
       21.21         3.45         3.39        18.38         5.19         6.44 
TCGA-R5-A7O7 TCGA-RD-A8N6 TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PU 
       45.67         8.94        18.48        46.26        13.35        27.35 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA68 
       14.33        18.74        52.24        64.18        22.09        40.08 
TCGA-VQ-AA6A TCGA-VQ-AA6D 
       32.94        17.13 

$`DEL PEAK 58(XP11.3) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       31.27        58.55         7.63         5.92        13.94        16.24 
TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT 
        7.69         6.21        33.27         2.63        18.64         9.30 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A6FD 
       14.86        14.50        12.16       122.10        60.39        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
        3.68        41.52        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43M TCGA-L5-A4OG 
        6.28         3.16        30.25         0.30         8.94         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       32.61        19.99         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         0.36         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       46.09        10.36        10.45        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 
       15.35         0.10        12.76        12.59         0.10        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33         4.47        12.33         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        5.06        14.70         7.04        29.59         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30        15.78         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EX 
        4.80        15.35        22.82        12.43         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       30.71        18.18        46.19        15.06        11.24         9.17 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        6.61         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        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-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        18.15        15.32        28.73 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.56        12.95         2.66         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       19.50         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        19.17        14.79         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        25.18        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        0.49        11.54        15.81        16.44        15.68         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        12.56         7.53         6.08         1.48        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-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-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         0.10         3.42         9.34        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        7.99        54.08         4.01        14.01        12.03         0.00 
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 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        79.07        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07        12.36        12.66        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 
       18.54        18.61        17.85        17.19        10.26        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       11.31        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        13.71        11.24        11.44         2.96 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6874 
       15.65         8.38         4.34         7.13        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-A5NB 
       22.29        17.06        59.54         5.03         0.56        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-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-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 
       10.19         0.26         2.10        19.36         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
        8.81        27.42        18.81         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51         5.56         1.81         7.82 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H 
       13.51         2.53         5.56        60.56        20.15        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73         9.86        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        48.79         5.46        13.25        13.02        35.24 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        29.98        54.12        26.04        16.14        21.11 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                        64.18                        122.30 
  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE 
                       13.015                        12.620 
[1] "0.1 - 64.2 (13.0)"  "0.0 - 122.3 (12.6)"
[1] "hr=" "1"  
D97V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 58(XP11.3) MUTATED         2        3        6        5        23
  DEL PEAK 58(XP11.3) WILD-TYPE       9       16       42       27        54
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 58(XP11.3) MUTATED          24        12         26         13
  DEL PEAK 58(XP11.3) WILD-TYPE        60        17         71         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 58(XP11.3) MUTATED            8        7         0
  DEL PEAK 58(XP11.3) WILD-TYPE         40       44         4
D97V3, multiclass
            clus
vv           DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             3                            16
  STAGE IB                             6                            42
  STAGE II                             5                            27
  STAGE IIA                           23                            54
  STAGE IIB                           24                            60
  STAGE III                           12                            17
  STAGE IIIA                          26                            71
  STAGE IIIB                          13                            59
  STAGE IIIC                           8                            40
  STAGE IV                             7                            44
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 58(XP11.3) MUTATED      11  30  70  21
  DEL PEAK 58(XP11.3) WILD-TYPE    42  96 210 103
D97V4, multiclass
       clus
vv      DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  T0+T1                          11                            42
  T2                             30                            96
  T3                             70                           210
  T4                             21                           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 58(XP11.3) MUTATED    48  45  23  15
  DEL PEAK 58(XP11.3) WILD-TYPE 152 137  73  82
D97V5, multiclass
    clus
vv   DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  N0                          48                           152
  N1                          45                           137
  N2                          23                            73
  N3                          15                            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V6, binary
                               cls
clus                              0   1
  DEL PEAK 58(XP11.3) MUTATED   116   6
  DEL PEAK 58(XP11.3) WILD-TYPE 397  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 58(XP11.3) MUTATED    116    6
  DEL PEAK 58(XP11.3) WILD-TYPE  397   33
   clus
vv  DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  0                         116                           397
  1                           6                            33
[1] 2 2
[1] FALSE
D97V7, binary
                               cls
clus                              0   1
  DEL PEAK 58(XP11.3) MUTATED    29 109
  DEL PEAK 58(XP11.3) WILD-TYPE 153 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 58(XP11.3) MUTATED     29  109
  DEL PEAK 58(XP11.3) WILD-TYPE  153  318
        clus
vv       DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  FEMALE                          29                           153
  MALE                           109                           318
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 58(XP11.3) MUTATED                                       9
  DEL PEAK 58(XP11.3) WILD-TYPE                                    62
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 58(XP11.3) MUTATED                                                       21
  DEL PEAK 58(XP11.3) WILD-TYPE                                                    141
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 58(XP11.3) MUTATED                                                                  13
  DEL PEAK 58(XP11.3) WILD-TYPE                                                                68
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 58(XP11.3) MUTATED                                                 19
  DEL PEAK 58(XP11.3) WILD-TYPE                                               59
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 58(XP11.3) MUTATED                                                          2
  DEL PEAK 58(XP11.3) WILD-TYPE                                                       19
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 58(XP11.3) MUTATED                                                           1
  DEL PEAK 58(XP11.3) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 58(XP11.3) MUTATED                                          4
  DEL PEAK 58(XP11.3) WILD-TYPE                                        9
D97V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 58(XP11.3) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    4
                                                                   clus
vv                                                                  DEL PEAK 58(XP11.3) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V9, binary
                               cls
clus                              0   1
  DEL PEAK 58(XP11.3) MUTATED     1 137
  DEL PEAK 58(XP11.3) WILD-TYPE   5 466
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 58(XP11.3) MUTATED      1  137
  DEL PEAK 58(XP11.3) WILD-TYPE    5  466
     clus
vv    DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  NO                            1                             5
  YES                         137                           466
[1] 2 2
[1] FALSE
D97V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 58(XP11.3) MUTATED    52   4   3   2
  DEL PEAK 58(XP11.3) WILD-TYPE 295  14  16  23
D97V11, multiclass
    clus
vv   DEL PEAK 58(XP11.3) MUTATED DEL PEAK 58(XP11.3) WILD-TYPE
  R0                          52                           295
  R1                           4                            14
  R2                           3                            16
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 58(XP11.3) MUTATED      37                         1
  DEL PEAK 58(XP11.3) WILD-TYPE    92                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 58(XP11.3) MUTATED                                           0    82
  DEL PEAK 58(XP11.3) WILD-TYPE                                         1   303
D97V13, multiclass
                                           clus
vv                                          DEL PEAK 58(XP11.3) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              82
                                           clus
vv                                          DEL PEAK 58(XP11.3) WILD-TYPE
  ASIAN                                                                92
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V14, binary
                               cls
clus                              0   1
  DEL PEAK 58(XP11.3) MUTATED     2  87
  DEL PEAK 58(XP11.3) WILD-TYPE   5 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 58(XP11.3) MUTATED      2   87
  DEL PEAK 58(XP11.3) WILD-TYPE    5  307
                        clus
vv                       DEL PEAK 58(XP11.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       DEL PEAK 58(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           307
[1] 2 2
[1] FALSE

Clustering(98) Variable = DEL PEAK 59(XQ11.2) MUTATION ANALYSIS
D98V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 59(XQ11.2) MUTATED    59  37
  DEL PEAK 59(XQ11.2) WILD-TYPE 295 184
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                           96                           479 
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                           37                           184 
$`DEL PEAK 59(XQ11.2) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IG-A3YC TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FH 
       25.78         4.21        20.12         9.96        44.75        42.77 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OJ 
       25.41        23.18         8.94        24.00         3.68        21.01 
TCGA-L5-A4OP TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.17         0.36         3.95        13.48        16.47        13.55 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49Y 
        8.71        13.41         5.92        10.45        12.66        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-M9-A5M8 TCGA-Q9-A6FU 
       12.49        22.39        25.25        10.52        33.11         5.16 
TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        1.45         5.29         3.42         9.27         4.44        18.81 
TCGA-VR-A8ER TCGA-VR-AA7B TCGA-X8-AAAR TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
       12.43        11.24        10.16        11.70        19.56         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8058 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 
       18.35        19.33        17.49        16.31        19.50        13.08 
TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       17.52        11.54        15.81        13.87         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A489 TCGA-CG-4300 
        1.48         1.15         0.07         0.13        11.31        20.02 
TCGA-CG-4301 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5718 
        3.02        29.98        47.05        19.07         7.07        36.00 
TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 
       15.02        19.13        15.22        15.98        12.79        18.21 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
        9.76         7.40         7.99        13.58         5.52         0.23 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP 
       12.30        21.21         3.39        18.38         1.41         6.44 
TCGA-IN-A6RR TCGA-RD-A8MV TCGA-RD-A8N6 TCGA-VQ-A8E0 TCGA-VQ-A8PS TCGA-VQ-A8PU 
        6.74       122.30         8.94        18.48        13.35        27.35 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       18.74        20.81        22.09        40.08        32.94        17.13 

$`DEL PEAK 59(XQ11.2) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IC-A6RF TCGA-IG-A3I8 
        8.94        16.24        32.45         7.69         6.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       20.09         0.85        20.78         2.63        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FB 
       14.86         4.67        14.50        12.16       122.10        60.39 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
       68.02         3.68        41.52        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J 
       24.03         6.28         3.16        30.25         0.30         4.31 
TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
        4.70        32.61        19.99        47.93        18.35         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        1.38         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.43         6.94         8.71         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NL 
        3.02        55.50         2.66        35.97        12.92        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        27.12        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       46.09        10.36        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 
       15.35         0.10        13.25         0.10        12.59        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
        4.47        12.33        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13         7.82         8.02         7.59         5.06        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        29.59         6.35        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RE 
        2.89        12.69         7.00        20.02        20.38         4.80 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        19.96        22.82         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
        9.17        15.91         3.42         2.10         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        7.43        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        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-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         7.40         6.18         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 
        9.34        13.45         6.28         7.53         0.49        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
        9.86        15.68         8.22        10.68        12.56         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-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-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-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-A487 TCGA-CD-A48A 
        0.10         0.13         0.10         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       11.61         6.58        12.20         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-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-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        12.03        21.99         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        17.19        10.26        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.56        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        23.84         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       27.42         3.45        18.81         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51         5.56         1.81         7.82        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG 
        2.53         5.56        60.56        20.15        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73         9.86        45.67        18.21         8.52        61.25 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79         5.46        13.25        13.02        35.24        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       34.45        27.88        32.48         7.73        28.96        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        65.16        36.69        11.70        11.93 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        22.68         1.71        36.16         7.36         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        52.24         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
        6.58         5.72        64.18        21.04         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        28.41        29.98        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        21.11        12.43        10.62         0.79 

  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                        122.3                         122.1 
  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE 
                        13.38                         12.66 
[1] "0.1 - 122.3 (13.4)" "0.0 - 122.1 (12.7)"
[1] "hr=" "1"  
D98V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 59(XQ11.2) MUTATED         2        3        5        5        12
  DEL PEAK 59(XQ11.2) WILD-TYPE       9       16       43       27        65
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 59(XQ11.2) MUTATED          15         6         16          9
  DEL PEAK 59(XQ11.2) WILD-TYPE        69        23         81         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 59(XQ11.2) MUTATED            8        6         0
  DEL PEAK 59(XQ11.2) WILD-TYPE         40       45         4
D98V3, multiclass
            clus
vv           DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  STAGE I                              2                             9
  STAGE IA                             3                            16
  STAGE IB                             5                            43
  STAGE II                             5                            27
  STAGE IIA                           12                            65
  STAGE IIB                           15                            69
  STAGE III                            6                            23
  STAGE IIIA                          16                            81
  STAGE IIIB                           9                            63
  STAGE IIIC                           8                            40
  STAGE IV                             6                            45
  STAGE IVA                            0                             4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 59(XQ11.2) MUTATED      10  23  41  19
  DEL PEAK 59(XQ11.2) WILD-TYPE    43 103 239 105
D98V4, multiclass
       clus
vv      DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  T0+T1                          10                            43
  T2                             23                           103
  T3                             41                           239
  T4                             19                           105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 59(XQ11.2) MUTATED    29  30  19  14
  DEL PEAK 59(XQ11.2) WILD-TYPE 171 152  77  83
D98V5, multiclass
    clus
vv   DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  N0                          29                           171
  N1                          30                           152
  N2                          19                            77
  N3                          14                            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"
D98V6, binary
                               cls
clus                              0   1
  DEL PEAK 59(XQ11.2) MUTATED    81   3
  DEL PEAK 59(XQ11.2) WILD-TYPE 432  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 59(XQ11.2) MUTATED     81    3
  DEL PEAK 59(XQ11.2) WILD-TYPE  432   36
   clus
vv  DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  0                          81                           432
  1                           3                            36
[1] 2 2
[1] FALSE
D98V7, binary
                               cls
clus                              0   1
  DEL PEAK 59(XQ11.2) MUTATED    23  75
  DEL PEAK 59(XQ11.2) WILD-TYPE 159 352
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 59(XQ11.2) MUTATED     23   75
  DEL PEAK 59(XQ11.2) WILD-TYPE  159  352
        clus
vv       DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  FEMALE                          23                           159
  MALE                            75                           352
[1] 2 2
[1] FALSE
                               vv
clus                            STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 59(XQ11.2) MUTATED                                       8
  DEL PEAK 59(XQ11.2) WILD-TYPE                                    63
                               vv
clus                            STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 59(XQ11.2) MUTATED                                                       22
  DEL PEAK 59(XQ11.2) WILD-TYPE                                                    140
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 59(XQ11.2) MUTATED                                                                  11
  DEL PEAK 59(XQ11.2) WILD-TYPE                                                                70
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 59(XQ11.2) MUTATED                                                 13
  DEL PEAK 59(XQ11.2) WILD-TYPE                                               65
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 59(XQ11.2) MUTATED                                                          1
  DEL PEAK 59(XQ11.2) WILD-TYPE                                                       20
                               vv
clus                            STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 59(XQ11.2) MUTATED                                                           1
  DEL PEAK 59(XQ11.2) WILD-TYPE                                                         7
                               vv
clus                            STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 59(XQ11.2) MUTATED                                          3
  DEL PEAK 59(XQ11.2) WILD-TYPE                                       10
D98V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 59(XQ11.2) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                       8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                     22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                           13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                    1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                   1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                    3
                                                                   clus
vv                                                                  DEL PEAK 59(XQ11.2) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            70
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                             65
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                     7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     10
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V9, binary
                               cls
clus                              0   1
  DEL PEAK 59(XQ11.2) MUTATED     1  97
  DEL PEAK 59(XQ11.2) WILD-TYPE   5 506
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 59(XQ11.2) MUTATED      1   97
  DEL PEAK 59(XQ11.2) WILD-TYPE    5  506
     clus
vv    DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  NO                            1                             5
  YES                          97                           506
[1] 2 2
[1] FALSE
D98V10, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 59(XQ11.2) MUTATED    48   4   1   2
  DEL PEAK 59(XQ11.2) WILD-TYPE 299  14  18  23
D98V11, multiclass
    clus
vv   DEL PEAK 59(XQ11.2) MUTATED DEL PEAK 59(XQ11.2) WILD-TYPE
  R0                          48                           299
  R1                           4                            14
  R2                           1                            18
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V12, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 59(XQ11.2) MUTATED      18                         2
  DEL PEAK 59(XQ11.2) WILD-TYPE   111                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 59(XQ11.2) MUTATED                                           0    60
  DEL PEAK 59(XQ11.2) WILD-TYPE                                         1   325
D98V13, multiclass
                                           clus
vv                                          DEL PEAK 59(XQ11.2) MUTATED
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              60
                                           clus
vv                                          DEL PEAK 59(XQ11.2) WILD-TYPE
  ASIAN                                                               111
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V14, binary
                               cls
clus                              0   1
  DEL PEAK 59(XQ11.2) MUTATED     1  58
  DEL PEAK 59(XQ11.2) WILD-TYPE   6 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 59(XQ11.2) MUTATED      1   58
  DEL PEAK 59(XQ11.2) WILD-TYPE    6  336
                        clus
vv                       DEL PEAK 59(XQ11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK 59(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           336
[1] 2 2
[1] FALSE

Clustering(99) Variable = DEL PEAK 60(XQ21.33) MUTATION ANALYSIS
D99V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 60(XQ21.33) MUTATED    62  29
  DEL PEAK 60(XQ21.33) WILD-TYPE 292 192
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                            91                            484 
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                            29                            192 
$`DEL PEAK 60(XQ21.33) MUTATED`
TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-JY-A6FH TCGA-JY-A938 TCGA-L5-A43M 
       25.78         4.21         6.21        42.77        25.41         8.94 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A88Y TCGA-L5-A891 
       21.01        47.93         7.17         3.16         0.36         3.95 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49M TCGA-LN-A49W 
       13.48        16.47        13.55        13.22        12.66        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U7 
       12.46        12.49        22.39         0.10        11.54        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W8 
       10.52        12.03         0.13        33.11         5.06         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        1.45         7.00         3.42         4.80         9.27         4.44 
TCGA-VR-A8EO TCGA-VR-AA7B TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
       18.81        11.24        19.73        11.70        19.56         9.44 
TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8058 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8365 
        9.21        28.01        17.49        16.31        19.50        17.52 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       11.54        15.81        13.87         7.53        22.26         1.48 
TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-A489 TCGA-CG-4300 
       13.51        13.15         0.07         0.13        11.31        20.02 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 
        3.02         7.99        29.98        47.05        19.07         7.07 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX 
       15.02        20.55        15.22        12.33        18.21        11.31 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-8211 TCGA-HU-A4H5 TCGA-HU-A4HD 
        9.76         7.40         7.99        13.58        12.30        27.42 
TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8P5 
       21.21        18.38         6.74        48.79        18.48         7.73 
TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A94U TCGA-VQ-AA6A 
       13.35        27.35        20.81         9.50        22.09        32.94 
TCGA-VQ-AA6D 
       17.13 

$`DEL PEAK 60(XQ21.33) WILD-TYPE`
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       31.27        14.30        58.55         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        8.94        16.24        32.45         7.69        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS 
        0.85        20.78         2.63        20.12        18.64         3.88 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        9.30         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FB TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       44.75        60.39        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       23.18        31.56        25.22        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       30.25         0.30         4.31        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        19.99        18.35         3.32         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88T 
        4.90        29.00         7.13         7.43         6.94         8.71 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.02        55.50         2.66 
TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       35.97        12.92         7.76         5.49        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.41        27.12        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 
       15.35         0.10         0.10        12.59        12.76        12.59 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW 
       15.52        12.33        13.22         4.47        12.33        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.23        13.18         5.16         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       14.70         7.04        29.59         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BV TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV 
       15.78        12.69        20.02        20.38         5.29        15.35 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       19.96        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       28.11        30.71        18.18        42.87        46.19        15.06 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
        9.17        15.91        10.16         3.42         2.10         2.66 
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        7.43        18.35        30.90         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
       34.68        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       39.12        26.10         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82        24.76        35.24        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       18.15        15.32        28.73        12.43         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        14.43        11.44         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        20.55         8.05         0.56        12.95         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        19.17        14.79         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         9.34        13.45         6.28         7.53         0.49 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         9.86        15.68         8.22        10.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        13.41        13.51        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83         3.25        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.13         0.13         0.10         3.42         9.34        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       11.61         6.58        12.20         0.10        12.62        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       12.03        21.99         0.00         9.01        18.97        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         5.52         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.88         8.81         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
        5.19        13.08         1.41         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        5.56         1.81         7.82        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
       60.56        20.15        37.64         3.72        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        35.24        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        26.24        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       65.16        36.69        11.70        11.93        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       22.68         1.71        36.16         7.36         9.73        52.24 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       64.18        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       40.08        28.41        29.98        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                         48.79                         122.30 
  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE 
                         13.15                          12.76 
[1] "0.1 - 48.8 (13.2)"  "0.0 - 122.3 (12.8)"
[1] "hr=" "1.1"
D99V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 60(XQ21.33) MUTATED         2        5        8        6        13
  DEL PEAK 60(XQ21.33) WILD-TYPE       9       14       40       26        64
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 60(XQ21.33) MUTATED          10         7         13          8
  DEL PEAK 60(XQ21.33) WILD-TYPE        74        22         84         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 60(XQ21.33) MUTATED            5        7         0
  DEL PEAK 60(XQ21.33) WILD-TYPE         43       44         4
D99V3, multiclass
            clus
vv           DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  STAGE I                               2                              9
  STAGE IA                              5                             14
  STAGE IB                              8                             40
  STAGE II                              6                             26
  STAGE IIA                            13                             64
  STAGE IIB                            10                             74
  STAGE III                             7                             22
  STAGE IIIA                           13                             84
  STAGE IIIB                            8                             64
  STAGE IIIC                            5                             43
  STAGE IV                              7                             44
  STAGE IVA                             0                              4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 60(XQ21.33) MUTATED      10  21  43  14
  DEL PEAK 60(XQ21.33) WILD-TYPE    43 105 237 110
D99V4, multiclass
       clus
vv      DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  T0+T1                           10                             43
  T2                              21                            105
  T3                              43                            237
  T4                              14                            110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 60(XQ21.33) MUTATED    37  25  13  11
  DEL PEAK 60(XQ21.33) WILD-TYPE 163 157  83  86
D99V5, multiclass
    clus
vv   DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  N0                           37                            163
  N1                           25                            157
  N2                           13                             83
  N3                           11                             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V6, binary
                                cls
clus                               0   1
  DEL PEAK 60(XQ21.33) MUTATED    76   4
  DEL PEAK 60(XQ21.33) WILD-TYPE 437  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 60(XQ21.33) MUTATED     76    4
  DEL PEAK 60(XQ21.33) WILD-TYPE  437   35
   clus
vv  DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  0                           76                            437
  1                            4                             35
[1] 2 2
[1] FALSE
D99V7, binary
                                cls
clus                               0   1
  DEL PEAK 60(XQ21.33) MUTATED    24  70
  DEL PEAK 60(XQ21.33) WILD-TYPE 158 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 60(XQ21.33) MUTATED     24   70
  DEL PEAK 60(XQ21.33) WILD-TYPE  158  357
        clus
vv       DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  FEMALE                           24                            158
  MALE                             70                            357
[1] 2 2
[1] FALSE
                                vv
clus                             STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  DEL PEAK 60(XQ21.33) MUTATED                                       8
  DEL PEAK 60(XQ21.33) WILD-TYPE                                    63
                                vv
clus                             STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 60(XQ21.33) MUTATED                                                       18
  DEL PEAK 60(XQ21.33) WILD-TYPE                                                    144
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 60(XQ21.33) MUTATED                                                                  12
  DEL PEAK 60(XQ21.33) WILD-TYPE                                                                69
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  DEL PEAK 60(XQ21.33) MUTATED                                                 11
  DEL PEAK 60(XQ21.33) WILD-TYPE                                               67
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  DEL PEAK 60(XQ21.33) MUTATED                                                          3
  DEL PEAK 60(XQ21.33) WILD-TYPE                                                       18
                                vv
clus                             STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  DEL PEAK 60(XQ21.33) MUTATED                                                           2
  DEL PEAK 60(XQ21.33) WILD-TYPE                                                         6
                                vv
clus                             STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  DEL PEAK 60(XQ21.33) MUTATED                                          1
  DEL PEAK 60(XQ21.33) WILD-TYPE                                       12
D99V8, multiclass
                                                                   clus
vv                                                                  DEL PEAK 60(XQ21.33) MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                        8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                            11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                     3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                    2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                     1
                                                                   clus
vv                                                                  DEL PEAK 60(XQ21.33) WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                                         63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                                       144
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                             69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                              67
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                                      18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                                      6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                                      12
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V9, binary
                                cls
clus                               0   1
  DEL PEAK 60(XQ21.33) MUTATED     1  93
  DEL PEAK 60(XQ21.33) WILD-TYPE   5 510
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 60(XQ21.33) MUTATED      1   93
  DEL PEAK 60(XQ21.33) WILD-TYPE    5  510
     clus
vv    DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  NO                             1                              5
  YES                           93                            510
[1] 2 2
[1] FALSE
D99V10, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 60(XQ21.33) MUTATED    46   3   1   1
  DEL PEAK 60(XQ21.33) WILD-TYPE 301  15  18  24
D99V11, multiclass
    clus
vv   DEL PEAK 60(XQ21.33) MUTATED DEL PEAK 60(XQ21.33) WILD-TYPE
  R0                           46                            301
  R1                            3                             15
  R2                            1                             18
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 60(XQ21.33) MUTATED      20                         2
  DEL PEAK 60(XQ21.33) WILD-TYPE   109                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 60(XQ21.33) MUTATED                                           0
  DEL PEAK 60(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 60(XQ21.33) MUTATED      56
  DEL PEAK 60(XQ21.33) WILD-TYPE   329
D99V13, multiclass
                                           clus
vv                                          DEL PEAK 60(XQ21.33) MUTATED
  ASIAN                                                               20
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               56
                                           clus
vv                                          DEL PEAK 60(XQ21.33) WILD-TYPE
  ASIAN                                                                109
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V14, binary
                                cls
clus                               0   1
  DEL PEAK 60(XQ21.33) MUTATED     0  56
  DEL PEAK 60(XQ21.33) WILD-TYPE   7 338
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 60(XQ21.33) MUTATED      0   56
  DEL PEAK 60(XQ21.33) WILD-TYPE    7  338
                        clus
vv                       DEL PEAK 60(XQ21.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       DEL PEAK 60(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            338
[1] 2 2
[1] FALSE
