[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/22507048/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532764/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=625, common to both=625
[1]  94 625
[1] "AMP PEAK  1(1P36.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                           101                            524 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                           101                            524 
[1] "AMP PEAK  2(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           95                           530 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           95                           530 
[1] "AMP PEAK  3(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          249                           376 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          249                           376 
[1] "AMP PEAK  4(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          244                           381 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          244                           381 
[1] "AMP PEAK  5(2Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          155                           470 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          155                           470 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          287                           338 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          287                           338 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           228                            397 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           228                            397 
[1] "AMP PEAK  8(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          216                           409 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          216                           409 
[1] "AMP PEAK  9(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          192                           433 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          192                           433 
[1] "AMP PEAK 10(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        141                         484 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        141                         484 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        111                         514 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        111                         514 
[1] "AMP PEAK 12(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          353                           272 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          353                           272 
[1] "AMP PEAK 13(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          339                           286 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          339                           286 
[1] "AMP PEAK 14(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          317                           308 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          317                           308 
[1] "AMP PEAK 15(8P23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          229                           396 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          229                           396 
[1] "AMP PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           272                            353 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           272                            353 
[1] "AMP PEAK 17(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           454                            171 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           454                            171 
[1] "AMP PEAK 18(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           91                           534 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           91                           534 
[1] "AMP PEAK 19(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          132                           493 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          132                           493 
[1] "AMP PEAK 20(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          185                           440 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          185                           440 
[1] "AMP PEAK 21(10P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            169                             456 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            169                             456 
[1] "AMP PEAK 22(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           125                            500 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           125                            500 
[1] "AMP PEAK 23(10Q26.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            119                             506 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            119                             506 
[1] "AMP PEAK 24(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         138                          487 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         138                          487 
[1] "AMP PEAK 25(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           218                            407 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           218                            407 
[1] "AMP PEAK 26(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           207                            418 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           207                            418 
[1] "AMP PEAK 27(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         161                          464 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         161                          464 
[1] "AMP PEAK 28(13Q12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           216                            409 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           216                            409 
[1] "AMP PEAK 29(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           243                            382 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           243                            382 
[1] "AMP PEAK 30(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           113                            512 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           113                            512 
[1] "AMP PEAK 31(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           168                            457 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           168                            457 
[1] "AMP PEAK 32(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         222                          403 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         222                          403 
[1] "AMP PEAK 33(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            178                             447 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            178                             447 
[1] "AMP PEAK 34(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           198                            427 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           198                            427 
[1] "AMP PEAK 35(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                         185                          440 
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                         185                          440 
[1] "AMP PEAK 36(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                            164                             461 
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                            164                             461 
[1] "AMP PEAK 37(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                           416                            209 
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                           416                            209 
[1] "AMP PEAK 38(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                        155                         470 
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                        155                         470 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           210                            415 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           210                            415 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          156                           469 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          156                           469 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         46                         579 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         46                         579 
[1] "DEL PEAK  4(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         43                         582 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         43                         582 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          126                           499 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          126                           499 
[1] "DEL PEAK  6(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           87                           538 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           87                           538 
[1] "DEL PEAK  7(2Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           85                           540 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           85                           540 
[1] "DEL PEAK  8(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          122                           503 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          122                           503 
[1] "DEL PEAK  9(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          250                           375 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          250                           375 
[1] "DEL PEAK 10(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          282                           343 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          282                           343 
[1] "DEL PEAK 11(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           98                           527 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           98                           527 
[1] "DEL PEAK 12(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            65                            560 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            65                            560 
[1] "DEL PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          271                           354 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          271                           354 
[1] "DEL PEAK 14(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          269                           356 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          269                           356 
[1] "DEL PEAK 15(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          298                           327 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          298                           327 
[1] "DEL PEAK 16(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          300                           325 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          300                           325 
[1] "DEL PEAK 17(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          282                           343 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          282                           343 
[1] "DEL PEAK 18(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          188                           437 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          188                           437 
[1] "DEL PEAK 19(6Q16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          147                           478 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          147                           478 
[1] "DEL PEAK 20(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        152                         473 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        152                         473 
[1] "DEL PEAK 21(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          127                           498 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          127                           498 
[1] "DEL PEAK 22(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          165                           460 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          165                           460 
[1] "DEL PEAK 23(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          214                           411 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          214                           411 
[1] "DEL PEAK 24(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        302                         323 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        302                         323 
[1] "DEL PEAK 25(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          334                           291 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          334                           291 
[1] "DEL PEAK 26(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           175                            450 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           175                            450 
[1] "DEL PEAK 27(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           131                            494 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           131                            494 
[1] "DEL PEAK 28(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                            102                             523 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                            102                             523 
[1] "DEL PEAK 29(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                           135                            490 
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                           135                            490 
[1] "DEL PEAK 30(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                            183                             442 
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                            183                             442 
[1] "DEL PEAK 31(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                           175                            450 
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                           175                            450 
[1] "DEL PEAK 32(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                         178                          447 
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                         178                          447 
[1] "DEL PEAK 33(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                           113                            512 
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                           113                            512 
[1] "DEL PEAK 34(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                           110                            515 
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                           110                            515 
[1] "DEL PEAK 35(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                            138                             487 
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                            138                             487 
[1] "DEL PEAK 36(13Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                            126                             499 
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                            126                             499 
[1] "DEL PEAK 37(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                           187                            438 
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                           187                            438 
[1] "DEL PEAK 38(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                           183                            442 
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                           183                            442 
[1] "DEL PEAK 39(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                           177                            448 
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                           177                            448 
[1] "DEL PEAK 40(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                           153                            472 
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                           153                            472 
[1] "DEL PEAK 41(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                           265                            360 
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                           265                            360 
[1] "DEL PEAK 42(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                         267                          358 
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                         267                          358 
[1] "DEL PEAK 43(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                           103                            522 
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                           103                            522 
[1] "DEL PEAK 44(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                           292                            333 
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                           292                            333 
[1] "DEL PEAK 45(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                           323                            302 
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                           323                            302 
[1] "DEL PEAK 46(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                           249                            376 
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                           249                            376 
[1] "DEL PEAK 47(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            72                            553 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            72                            553 
[1] "DEL PEAK 48(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           286                            339 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           286                            339 
[1] "DEL PEAK 49(21Q22.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                            305                             320 
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                            305                             320 
[1] "DEL PEAK 50(22Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                           230                            395 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                           230                            395 
[1] "DEL PEAK 51(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                            235                             390 
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                            235                             390 
[1] "DEL PEAK 52(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                          151                           474 
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                          151                           474 
[1] "DEL PEAK 53(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                          146                           479 
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                          146                           479 
[1] "DEL PEAK 54(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                          148                           477 
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                          148                           477 
[1] "DEL PEAK 55(XQ11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                          105                           520 
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                          105                           520 
[1] "DEL PEAK 56(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                            98                            527 
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                            98                            527 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"              "VITAL_STATUS"               
 [3] "DAYS_TO_DEATH"               "DAYS_TO_LAST_FOLLOWUP"      
 [5] "PATHOLOGIC_STAGE"            "PATHOLOGY_T_STAGE"          
 [7] "PATHOLOGY_N_STAGE"           "PATHOLOGY_M_STAGE"          
 [9] "GENDER"                      "RADIATION_THERAPY"          
[11] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
[13] "RACE"                        "ETHNICITY"                  

Input Data has 14 rows and 625 columns.

[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=215,	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=298,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 625 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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  54 136 283 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   55   136   283   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  54 136 283 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   55   136   283   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
207 187  98  96 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
207 187  98  96 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
207 187  98  96 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
207 187  98  96 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=46, 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    57  39
  AMP PEAK  1(1P36.22) WILD-TYPE 297 206
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            96                            503 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                            39                            206 
$`AMP PEAK  1(1P36.22) MUTATED`
TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-IC-A6RE TCGA-IG-A3YA 
        0.36        20.02        47.05        22.98         7.69        20.78 
TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-JY-A93E 
        3.88        17.03         0.79         4.67        47.38        25.22 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
       47.93        18.35         3.16         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NS TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        2.66        13.48        13.41        10.85        10.45        12.66 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6L4 
       13.15        12.59        12.62         0.13         8.02        16.31 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-VR-AA7B 
       38.40        53.95         9.30        15.78        12.69        11.24 
TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7901 TCGA-BR-8286 
        2.10        58.03         6.61         9.21         3.45        29.42 
TCGA-BR-8289 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 
        2.66        25.18        12.79        34.98         0.72        13.51 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4443 TCGA-CG-4449 
       13.02        13.35        12.43        12.20        29.98        19.07 
TCGA-CG-5718 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-A4YU 
       36.00        69.04        18.54        10.26        15.22        16.44 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GH 
       11.24        22.29        19.53        30.51        26.47        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
        8.98         6.58        33.40        36.36         3.45        18.38 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A805 
        6.44         6.74        11.70         2.53        14.04         9.24 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8E0 
        8.61        16.67        37.91       115.69         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91U 
       43.36        22.19        17.85         1.87        64.57         1.71 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        4.54        66.81        42.54        18.41        38.93        17.13 

$`AMP PEAK  1(1P36.22) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
        5.16        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        4.21        32.45        33.27        35.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 
       20.12        18.64         9.30         0.53        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
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-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        21.01         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       25.12         7.40        12.92        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37         8.71        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       46.09        10.36         5.92        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.38        15.35        13.25        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        12.85        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.59         5.06         7.04         6.35         2.89         2.30 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        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        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         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-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       29.56        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       29.59         9.60        32.25         8.05         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        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 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
        1.15        21.44        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       18.97         7.07        12.00        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-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-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        17.19        15.98        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-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 
       36.43        13.78        14.76        26.43        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       52.21         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       14.07        15.68        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53        12.59         6.51        10.62        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-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        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-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-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       42.64        60.85         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                          0.13                           0.00 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                        115.69                         122.30 
  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE 
                        13.445                         14.040 
[1] "0.1 - 115.7 (13.4)" "0.0 - 122.3 (14.0)"
[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        7        7        10
  AMP PEAK  1(1P36.22) WILD-TYPE       8       15       40       26        77
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1P36.22) MUTATED          13         1         16         13
  AMP PEAK  1(1P36.22) WILD-TYPE        74        27         79         59
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  1(1P36.22) MUTATED            5        5         2
  AMP PEAK  1(1P36.22) WILD-TYPE         41       44         2
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  STAGE I                               2                              8
  STAGE IA                              6                             15
  STAGE IB                              7                             40
  STAGE II                              7                             26
  STAGE IIA                            10                             77
  STAGE IIB                            13                             74
  STAGE III                             1                             27
  STAGE IIIA                           16                             79
  STAGE IIIB                           13                             59
  STAGE IIIC                            5                             41
  STAGE IV                              5                             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
  AMP PEAK  1(1P36.22) MUTATED      14  21  45  13
  AMP PEAK  1(1P36.22) WILD-TYPE    41 115 238 111
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  T0+T1                           14                             41
  T2                              21                            115
  T3                              45                            238
  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    31  29  16  16
  AMP PEAK  1(1P36.22) WILD-TYPE 176 158  82  80
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  N0                           31                            176
  N1                           29                            158
  N2                           16                             82
  N3                           16                             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"
D1V6, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    79   5
  AMP PEAK  1(1P36.22) WILD-TYPE 445  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     79    5
  AMP PEAK  1(1P36.22) WILD-TYPE  445   34
   clus
vv  AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  0                           79                            445
  1                            5                             34
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    16  85
  AMP PEAK  1(1P36.22) WILD-TYPE 169 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     16   85
  AMP PEAK  1(1P36.22) WILD-TYPE  169  355
        clus
vv       AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  FEMALE                           16                            169
  MALE                             85                            355
[1] 2 2
[1] FALSE
D1V8, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED    64  25
  AMP PEAK  1(1P36.22) WILD-TYPE 381  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED     64   25
  AMP PEAK  1(1P36.22) WILD-TYPE  381   94
     clus
vv    AMP PEAK  1(1P36.22) MUTATED AMP PEAK  1(1P36.22) WILD-TYPE
  NO                            64                            381
  YES                           25                             94
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P36.22) MUTATED      19                         2
  AMP PEAK  1(1P36.22) WILD-TYPE   115                        15
                                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      69
  AMP PEAK  1(1P36.22) WILD-TYPE   323
D1V11, multiclass
                                           clus
vv                                          AMP PEAK  1(1P36.22) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               69
                                           clus
vv                                          AMP PEAK  1(1P36.22) WILD-TYPE
  ASIAN                                                                115
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                323
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK  1(1P36.22) MUTATED     3  63
  AMP PEAK  1(1P36.22) WILD-TYPE   8 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.22) MUTATED      3   63
  AMP PEAK  1(1P36.22) WILD-TYPE    8  341
                        clus
vv                       AMP PEAK  1(1P36.22) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       AMP PEAK  1(1P36.22) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            341
[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    53  39
  AMP PEAK  2(1P34.2) WILD-TYPE 301 206
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           92                           507 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           39                           206 
$`AMP PEAK  2(1P34.2) MUTATED`
TCGA-L5-A88Y TCGA-CG-4444 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-2H-A9GN TCGA-IG-A3YA 
        0.36        47.05        16.24        27.35         8.94        20.78 
TCGA-IG-A51D TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A93E TCGA-L5-A4OM TCGA-L5-A4ON 
       17.03         4.67       122.10        25.22        47.93        18.35 
TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NL 
        1.38         7.13         3.75         3.02         2.66        13.22 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W 
        5.49        13.41        10.85        10.45        13.15        13.25 
TCGA-LN-A49X TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6DN 
       12.62        11.54        12.03         0.13        12.03         8.02 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-V5-A7RC TCGA-VR-A8EP 
       38.40         6.35        53.95        12.69         3.42        27.09 
TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       22.82        28.11        11.24        25.08         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 
       29.42        25.18        12.79         0.72        13.51        20.65 
TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A48A TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 
       21.44        12.59        12.43        20.91        18.54        10.26 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 
       18.21        14.27        16.44        11.38        19.53        17.06 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       63.06        26.47         5.92        25.81        11.77         8.98 
TCGA-HU-A4GU TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 
        6.58        18.38         6.44         6.74        11.70        63.62 
TCGA-R5-A7ZR TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-VQ-A8DU TCGA-VQ-A8E0 
        6.08       122.30       115.69        71.38         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PH TCGA-VQ-A8PZ TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-AA64 
       43.36        12.79        73.41         9.04        42.54        18.41 
TCGA-VQ-AA6A TCGA-VQ-AA6D 
       38.93        17.13 

$`AMP PEAK  2(1P34.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX 
        5.16        20.02        21.99        22.98        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63         5.92        13.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30         0.53         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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30        26.33        32.61        21.01         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        2.60        25.12         7.40        55.50        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       16.47        13.55         7.76        21.37         8.71        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-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       13.41        12.33        13.38        15.35        12.59        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        12.85 
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-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       13.18        12.85        12.26        33.11         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        5.06        16.31         7.04         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        2.30         7.00        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        9.27         8.98        25.81        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        18.21        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        58.03        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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 
        4.08         4.08         9.34         9.67         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        9.60        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         3.72         5.39         9.21        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.33        24.72        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 
        7.99        14.47        72.23        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-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        6.21        77.29        52.21        30.51         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       22.75        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
       18.81         3.39        12.46        13.35        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        15.75        13.51         2.53         5.56 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13        16.67        37.91        40.64       116.38 
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        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        55.56         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-AA68 
        5.72        66.81        21.04         2.66        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                         0.13                          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 
                        13.33                         14.04 
[1] "0.1 - 122.3 (13.3)" "0.0 - 116.4 (14.0)"
[1] "hr=" "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        12
  AMP PEAK  2(1P34.2) WILD-TYPE       7       19       45       29        75
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(1P34.2) MUTATED          12         7         18         11
  AMP PEAK  2(1P34.2) WILD-TYPE        75        21         77         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  2(1P34.2) MUTATED            5        3         2
  AMP PEAK  2(1P34.2) WILD-TYPE         41       46         2
D2V3, multiclass
            clus
vv           AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                             2                            19
  STAGE IB                             2                            45
  STAGE II                             4                            29
  STAGE IIA                           12                            75
  STAGE IIB                           12                            75
  STAGE III                            7                            21
  STAGE IIIA                          18                            77
  STAGE IIIB                          11                            61
  STAGE IIIC                           5                            41
  STAGE IV                             3                            46
  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  15  44  14
  AMP PEAK  2(1P34.2) WILD-TYPE    43 121 239 110
D2V4, multiclass
       clus
vv      AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  T0+T1                          12                            43
  T2                             15                           121
  T3                             44                           239
  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    25  33  14  12
  AMP PEAK  2(1P34.2) WILD-TYPE 182 154  84  84
D2V5, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  N0                          25                           182
  N1                          33                           154
  N2                          14                            84
  N3                          12                            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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    77   3
  AMP PEAK  2(1P34.2) WILD-TYPE 447  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     77    3
  AMP PEAK  2(1P34.2) WILD-TYPE  447   36
   clus
vv  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  0                          77                           447
  1                           3                            36
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    22  73
  AMP PEAK  2(1P34.2) WILD-TYPE 163 367
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     22   73
  AMP PEAK  2(1P34.2) WILD-TYPE  163  367
        clus
vv       AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  FEMALE                          22                           163
  MALE                            73                           367
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    56  30
  AMP PEAK  2(1P34.2) WILD-TYPE 389  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     56   30
  AMP PEAK  2(1P34.2) WILD-TYPE  389   89
     clus
vv    AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  NO                           56                           389
  YES                          30                            89
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1P34.2) MUTATED      19                         5
  AMP PEAK  2(1P34.2) WILD-TYPE   115                        12
                               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   329
D2V11, multiclass
                                           clus
vv                                          AMP PEAK  2(1P34.2) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              63
                                           clus
vv                                          AMP PEAK  2(1P34.2) WILD-TYPE
  ASIAN                                                               115
  BLACK OR AFRICAN AMERICAN                                            12
  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"
D2V12, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED     2  60
  AMP PEAK  2(1P34.2) WILD-TYPE   9 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED      2   60
  AMP PEAK  2(1P34.2) WILD-TYPE    9  344
                        clus
vv                       AMP PEAK  2(1P34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       AMP PEAK  2(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           344
[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   140  97
  AMP PEAK  3(1Q21.3) WILD-TYPE 214 148
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          237                           362 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                           97                           148 
$`AMP PEAK  3(1Q21.3) MUTATED`
TCGA-L5-A4OI TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       19.99         0.36        20.02        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       16.24        26.93        31.27        58.55         7.63        13.94 
TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
       16.24         7.69        35.21         0.85         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93D TCGA-JY-A93E 
        4.67        14.50       122.10         3.68        31.56        25.22 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        32.61        21.01        47.93        18.35         7.17 
TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        4.90         7.43         2.60         7.40         3.75         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-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49U 
       13.41        52.57        10.85         5.92        10.45        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        13.25        12.59        12.49        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.22         4.47        12.33        12.00        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        8.02         5.06        16.31        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EQ 
       15.78        12.69        20.38         3.42        16.44        22.82 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
        8.12        28.11        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ 
        2.10         1.32         2.66        19.73        58.03        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 
        9.44         6.61         4.08         9.67        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 
       29.42         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 
        7.36         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        31.96         8.22         0.72        28.34        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5804 
       20.65        20.42         1.15        21.44        13.15        12.10 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 
       12.76        12.53        12.33        12.30        12.39        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.82         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.20         7.99        54.08        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 
       36.00        12.03         4.01        20.91        20.55        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV 
       12.33        24.72        19.50        14.27        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       11.31        22.29        15.65         0.62         7.99        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 
        3.48        14.07        13.58         0.56         5.52        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        22.75        25.81        11.77         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI 
        6.58        12.95        23.80        33.40         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-MX-A666 
       13.35         6.44         6.74        11.70        63.62        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       18.21         6.08         8.61        16.67       122.30       115.69 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY 
       43.36        21.73         2.70        17.85        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       73.41        39.45        18.74        20.81         1.71        42.64 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        9.73         4.54        66.81        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6K 
       43.66        38.93        12.43 

$`AMP PEAK  3(1Q21.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       24.00         4.70        22.82        35.97        27.12         5.16 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF 
       79.07         0.23        20.15         9.86        27.35        25.78 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       14.30         5.92         8.94         4.21        32.45        33.27 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I 
       20.78        20.12         9.30         9.96        14.86        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02        41.52        47.38        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OO 
       24.03         6.28         3.16        30.25        26.33         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        1.38         3.16        58.59        29.00         7.13        15.48 
TCGA-L5-A88W TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       25.12        13.48        13.55         7.76        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       83.24        46.09        10.36        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       12.33        13.38        13.15        12.62        12.46        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.59        22.39        12.85        15.52        25.25        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.23        12.03        33.11         7.82         7.59         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         2.89         2.30         7.00         5.29        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-B7-5816 TCGA-B7-5818 
       11.24         9.17        41.23         3.42        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 
       35.24        35.84        33.63        39.78        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
        9.60        32.25         8.05         0.56        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       25.05         3.72        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53         0.66        32.52         0.46        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 
       13.41        13.02        13.18        13.35        11.21        12.59 
TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 
        7.17        12.59        11.64        12.07        12.43        11.31 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       19.13        18.84        18.61        17.85        13.35        15.98 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       20.32         8.38         4.34        19.96         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-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-A9TM TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8602 
        5.03         6.21        77.29         1.51        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX 
       22.68        24.20        21.37        29.98         0.10        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       15.68        36.36        18.81         3.39        12.46        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 
        5.56        37.64        36.95         3.72        19.73        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24        11.05         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       16.87        19.04         5.79         0.92        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        13.35        29.59        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       32.88        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA69 
       55.43         6.58         5.72        21.04         2.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                         0.13                          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 
                       13.150                        15.415 
[1] "0.1 - 122.3 (13.2)" "0.0 - 116.4 (15.4)"
[1] "hr=" "1.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(1Q21.3) MUTATED         6        9       20        9        36
  AMP PEAK  3(1Q21.3) WILD-TYPE       4       12       27       24        51
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(1Q21.3) MUTATED          34        12         37         24
  AMP PEAK  3(1Q21.3) WILD-TYPE        53        16         58         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  3(1Q21.3) MUTATED           14       20         4
  AMP PEAK  3(1Q21.3) WILD-TYPE         32       29         0
D3V3, multiclass
            clus
vv           AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  STAGE I                              6                             4
  STAGE IA                             9                            12
  STAGE IB                            20                            27
  STAGE II                             9                            24
  STAGE IIA                           36                            51
  STAGE IIB                           34                            53
  STAGE III                           12                            16
  STAGE IIIA                          37                            58
  STAGE IIIB                          24                            48
  STAGE IIIC                          14                            32
  STAGE IV                            20                            29
  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      30  55 114  38
  AMP PEAK  3(1Q21.3) WILD-TYPE    25  81 169  86
D3V4, multiclass
       clus
vv      AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  T0+T1                          30                            25
  T2                             55                            81
  T3                            114                           169
  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    86  71  34  37
  AMP PEAK  3(1Q21.3) WILD-TYPE 121 116  64  59
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  N0                          86                           121
  N1                          71                           116
  N2                          34                            64
  N3                          37                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   202  17
  AMP PEAK  3(1Q21.3) WILD-TYPE 322  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    202   17
  AMP PEAK  3(1Q21.3) WILD-TYPE  322   22
   clus
vv  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  0                         202                           322
  1                          17                            22
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED    65 184
  AMP PEAK  3(1Q21.3) WILD-TYPE 120 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED     65  184
  AMP PEAK  3(1Q21.3) WILD-TYPE  120  256
        clus
vv       AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  FEMALE                          65                           120
  MALE                           184                           256
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   170  56
  AMP PEAK  3(1Q21.3) WILD-TYPE 275  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    170   56
  AMP PEAK  3(1Q21.3) WILD-TYPE  275   63
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  NO                          170                           275
  YES                          56                            63
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q21.3) MUTATED      61                         9
  AMP PEAK  3(1Q21.3) WILD-TYPE    73                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q21.3) MUTATED                                           1   148
  AMP PEAK  3(1Q21.3) WILD-TYPE                                         0   244
D3V11, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q21.3) MUTATED
  ASIAN                                                              61
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             148
                                           clus
vv                                          AMP PEAK  3(1Q21.3) WILD-TYPE
  ASIAN                                                                73
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED     4 165
  AMP PEAK  3(1Q21.3) WILD-TYPE   7 239
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED      4  165
  AMP PEAK  3(1Q21.3) WILD-TYPE    7  239
                        clus
vv                       AMP PEAK  3(1Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         165
                        clus
vv                       AMP PEAK  3(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           239
[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   137  98
  AMP PEAK  4(1Q42.3) WILD-TYPE 217 147
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          235                           364 
  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                           98                           147 
$`AMP PEAK  4(1Q42.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-CG-4460 TCGA-EQ-A4SO TCGA-2H-A9GF TCGA-2H-A9GH 
       60.39         0.36        21.99        16.24        25.78        31.27 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94         8.94        16.24         7.69        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12        18.64         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41        12.82         4.67        14.50       122.10         3.68 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       47.38        31.56        25.22         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX 
       47.93        18.35         7.17         1.38         4.90         7.43 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       12.92        13.22         5.49        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.36         5.92        10.45        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       13.25        12.49        12.76        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ 
       13.22         4.47        12.33        12.00        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.26         5.06        16.31        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       15.78        12.69        20.38         3.42        16.44         9.27 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7I 
        8.12        28.11        18.18        52.27        46.19        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       18.21        25.08        14.37         2.10         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
       58.03        11.01         6.61         4.08         9.67         6.18 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
       19.33         9.17        25.61         9.21        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 
       18.15        28.73        14.43        11.44         0.69         9.60 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66         2.20         7.40         6.18        31.10 
TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.04         7.36         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ 
        1.12        12.79        31.96         8.22         7.53        34.98 
TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72        28.34        13.51         0.46        20.42         1.15 
TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 
       13.15        12.10        12.76        12.59        12.33        12.39 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       15.39         6.31        12.30        11.61         6.58        12.20 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        7.99        54.08        19.07        18.97         7.07        12.00 
TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 
        1.02         4.01        12.66        20.91        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        10.26        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 
       24.72        19.50        16.44        11.31        22.29         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99        72.23         3.48        14.07         0.56         5.52 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       28.96         0.76         3.25        22.75        25.81        11.77 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL 
        0.10         6.51        12.95        33.40         3.45        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
       19.53         6.44        15.75        63.62        18.21         6.08 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
      122.30       115.69        35.61        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       13.02        18.48        43.36         7.73        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
       17.85        14.33        73.41        39.45        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D 
       32.88         9.73        55.56         9.04         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6D 
       21.04        42.54        11.24        18.41        38.93        17.13 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK  4(1Q42.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        47.05        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        9.86        27.35        26.93        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS 
        5.92         4.21        32.45        33.27        20.78         3.88 
TCGA-IG-A4QT TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
        9.30         9.96        14.86        12.16        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       41.52        21.70        23.18        24.03         6.28         3.16 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU 
       30.25        21.01         3.32         3.16        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.13        15.48        25.12        13.48        16.47        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M 
        7.76        21.37         8.71        13.41        83.24        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y 
       12.43        13.41        12.33        13.38        12.62        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        12.85        25.25        10.52 
TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
       12.03        33.11         7.82         8.02         7.59         7.04 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV 
        9.30         2.89         2.30         7.00         5.29        15.35 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 
       18.31        33.70        18.05        11.24         9.17        41.23 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        3.42         2.66        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
       29.59        32.25         8.05         0.56        19.96        15.58 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31         3.32        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        3.72        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       26.73        24.79        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13        13.87         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53         0.66        32.52 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.18        13.35        11.21        12.53         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 
       12.59        11.64        12.07        12.82        12.43        11.31 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         8.05         4.01        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       12.03         0.00         9.01        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       19.13        20.55        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       15.98        16.80        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        4.34        19.96         7.13        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8604 
        6.21        77.29        63.06         1.51        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       15.68        36.36        18.81         3.39        18.38        12.46 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
       14.04        45.67         8.52        74.53         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13        16.67        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44         8.94        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V 
       64.57        11.70        21.83        61.22         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       60.85         9.50         2.01        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
        2.66        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        17.26         0.79 

  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE 
                          0.1                           0.0 
  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 
                        12.95                         15.27 
[1] "0.1 - 122.3 (12.9)" "0.0 - 116.4 (15.3)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(1Q42.3) MUTATED         4       10       18       10        36
  AMP PEAK  4(1Q42.3) WILD-TYPE       6       11       29       23        51
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(1Q42.3) MUTATED          29        13         37         25
  AMP PEAK  4(1Q42.3) WILD-TYPE        58        15         58         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  4(1Q42.3) MUTATED           18       18         4
  AMP PEAK  4(1Q42.3) WILD-TYPE         28       31         0
D4V3, multiclass
            clus
vv           AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  STAGE I                              4                             6
  STAGE IA                            10                            11
  STAGE IB                            18                            29
  STAGE II                            10                            23
  STAGE IIA                           36                            51
  STAGE IIB                           29                            58
  STAGE III                           13                            15
  STAGE IIIA                          37                            58
  STAGE IIIB                          25                            47
  STAGE IIIC                          18                            28
  STAGE IV                            18                            31
  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      31  51 105  45
  AMP PEAK  4(1Q42.3) WILD-TYPE    24  85 178  79
D4V4, multiclass
       clus
vv      AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  T0+T1                          31                            24
  T2                             51                            85
  T3                            105                           178
  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    81  74  36  35
  AMP PEAK  4(1Q42.3) WILD-TYPE 126 113  62  61
D4V5, multiclass
    clus
vv   AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  N0                          81                           126
  N1                          74                           113
  N2                          36                            62
  N3                          35                            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   199  16
  AMP PEAK  4(1Q42.3) WILD-TYPE 325  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED    199   16
  AMP PEAK  4(1Q42.3) WILD-TYPE  325   23
   clus
vv  AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  0                         199                           325
  1                          16                            23
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED    59 185
  AMP PEAK  4(1Q42.3) WILD-TYPE 126 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED     59  185
  AMP PEAK  4(1Q42.3) WILD-TYPE  126  255
        clus
vv       AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  FEMALE                          59                           126
  MALE                           185                           255
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED   165  56
  AMP PEAK  4(1Q42.3) WILD-TYPE 280  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED    165   56
  AMP PEAK  4(1Q42.3) WILD-TYPE  280   63
     clus
vv    AMP PEAK  4(1Q42.3) MUTATED AMP PEAK  4(1Q42.3) WILD-TYPE
  NO                          165                           280
  YES                          56                            63
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(1Q42.3) MUTATED      62                        11
  AMP PEAK  4(1Q42.3) WILD-TYPE    72                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(1Q42.3) MUTATED                                           0   145
  AMP PEAK  4(1Q42.3) WILD-TYPE                                         1   247
D4V11, multiclass
                                           clus
vv                                          AMP PEAK  4(1Q42.3) MUTATED
  ASIAN                                                              62
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             145
                                           clus
vv                                          AMP PEAK  4(1Q42.3) WILD-TYPE
  ASIAN                                                                72
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q42.3) MUTATED     4 160
  AMP PEAK  4(1Q42.3) WILD-TYPE   7 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q42.3) MUTATED      4  160
  AMP PEAK  4(1Q42.3) WILD-TYPE    7  244
                        clus
vv                       AMP PEAK  4(1Q42.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK  4(1Q42.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           244
[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    91  58
  AMP PEAK  5(2Q12.2) WILD-TYPE 263 187
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                          149                           450 
  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                           58                           187 
$`AMP PEAK  5(2Q12.2) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 
       15.68         4.31         8.94        47.05        21.99        79.07 
TCGA-MX-A663 TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A5S3 
        9.86        13.94         8.94        16.24        35.21        23.41 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH 
       14.50        44.75        31.56        25.22         0.30        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX 
       47.93         3.32         1.38         3.16         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A56G 
        2.60         3.75        55.50         8.71        52.57        10.85 
TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
        5.92        12.33        13.38        13.15        13.25        12.62 
TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       12.49        12.85        12.33        25.25        12.00        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       12.33        13.18         0.13        12.85        12.26         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        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
        6.35        53.95        12.69        20.38         3.42        16.44 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D 
       15.35        25.81        27.09        28.11        33.70        46.19 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       18.21        25.08         3.42         2.10         1.32         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        21.90         9.21        35.24        33.63        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        12.76         6.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-5718 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       12.43        11.61        36.00        18.54        17.19        10.26 
TCGA-D7-6528 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       15.22        16.44        11.24         7.99        72.23         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8243 
       19.53        17.06         0.56         5.52         6.21         5.92 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH 
       28.96         0.76        24.30        24.26        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         6.58         2.10        12.95        23.84        23.80 
TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A93H 
        3.45        12.46        19.53        12.59        10.62        37.64 
TCGA-R5-A7O7 TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       45.67        16.67         5.46        43.36         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A92D TCGA-VQ-AA68 
       12.79        17.85        20.81         1.71        66.81        43.66 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        54.12        27.55        17.26         0.79 

$`AMP PEAK  5(2Q12.2) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       60.39        34.85        18.28        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       22.82         0.36        35.97        27.12         5.16        20.02 
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U 
       22.98        16.24         0.23        20.15        27.35        26.93 
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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        68.02         3.68        41.52        47.38 
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-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OT 
       26.33        21.01        18.35         7.17        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       29.00        15.48        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49        21.37        13.41        83.24        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49V 
       10.45        12.66        12.43        13.41        15.35        12.59 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.46        12.59        12.76        12.59        22.39        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX 
       11.54        12.33        13.22         4.47        10.52        12.23 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       13.18        13.38        12.03        33.11         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX 
        2.89         2.30         7.00         5.29         9.27         8.98 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ 
       22.82        12.43         1.55        18.31         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       52.27        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       14.37        19.73        58.03        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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
        4.08         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       26.10        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 
       40.21        30.90        31.20        44.94        36.16        35.84 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       33.21        37.25        14.43        11.44        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        8.05         0.56        29.42         2.66        19.96        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         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 
       31.27        14.79         7.36        25.05         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        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        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        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52         0.46        20.65         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43        12.30        11.31         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       13.35        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27        11.38        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       21.07         5.59        22.68        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        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       29.00        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39        18.38        13.35         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        14.04        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-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-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        32.88        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-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-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       28.41        38.93        17.13        26.04        16.14        12.43 

  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE 
                         0.13                          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 
                       12.950                        14.315 
[1] "0.1 - 79.1 (12.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(2Q12.2) MUTATED         1        9       10        7        27
  AMP PEAK  5(2Q12.2) WILD-TYPE       9       12       37       26        60
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(2Q12.2) MUTATED          29         7         14         12
  AMP PEAK  5(2Q12.2) WILD-TYPE        58        21         81         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  5(2Q12.2) MUTATED           11        6         2
  AMP PEAK  5(2Q12.2) WILD-TYPE         35       43         2
D5V3, multiclass
            clus
vv           AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             9                            12
  STAGE IB                            10                            37
  STAGE II                             7                            26
  STAGE IIA                           27                            60
  STAGE IIB                           29                            58
  STAGE III                            7                            21
  STAGE IIIA                          14                            81
  STAGE IIIB                          12                            60
  STAGE IIIC                          11                            35
  STAGE IV                             6                            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
  AMP PEAK  5(2Q12.2) MUTATED      16  33  76  17
  AMP PEAK  5(2Q12.2) WILD-TYPE    39 103 207 107
D5V4, multiclass
       clus
vv      AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  T0+T1                          16                            39
  T2                             33                           103
  T3                             76                           207
  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    55  46  19  20
  AMP PEAK  5(2Q12.2) WILD-TYPE 152 141  79  76
D5V5, multiclass
    clus
vv   AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  N0                          55                           152
  N1                          46                           141
  N2                          19                            79
  N3                          20                            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   121   7
  AMP PEAK  5(2Q12.2) WILD-TYPE 403  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED    121    7
  AMP PEAK  5(2Q12.2) WILD-TYPE  403   32
   clus
vv  AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  0                         121                           403
  1                           7                            32
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED    38 117
  AMP PEAK  5(2Q12.2) WILD-TYPE 147 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED     38  117
  AMP PEAK  5(2Q12.2) WILD-TYPE  147  323
        clus
vv       AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  FEMALE                          38                           147
  MALE                           117                           323
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED   112  30
  AMP PEAK  5(2Q12.2) WILD-TYPE 333  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED    112   30
  AMP PEAK  5(2Q12.2) WILD-TYPE  333   89
     clus
vv    AMP PEAK  5(2Q12.2) MUTATED AMP PEAK  5(2Q12.2) WILD-TYPE
  NO                          112                           333
  YES                          30                            89
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(2Q12.2) MUTATED      40                         7
  AMP PEAK  5(2Q12.2) WILD-TYPE    94                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(2Q12.2) MUTATED                                           0    94
  AMP PEAK  5(2Q12.2) WILD-TYPE                                         1   298
D5V11, multiclass
                                           clus
vv                                          AMP PEAK  5(2Q12.2) MUTATED
  ASIAN                                                              40
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              94
                                           clus
vv                                          AMP PEAK  5(2Q12.2) WILD-TYPE
  ASIAN                                                                94
  BLACK OR AFRICAN AMERICAN                                            10
  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"
D5V12, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q12.2) MUTATED     3 105
  AMP PEAK  5(2Q12.2) WILD-TYPE   8 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q12.2) MUTATED      3  105
  AMP PEAK  5(2Q12.2) WILD-TYPE    8  299
                        clus
vv                       AMP PEAK  5(2Q12.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       AMP PEAK  5(2Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           299
[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   166 112
  AMP PEAK  6(3Q26.2) WILD-TYPE 188 133
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          278                           321 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          112                           133 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT 
       15.68        60.39         4.31        24.00        35.97        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GH 
        5.16        47.05        16.24         0.23        27.35        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30        58.55         7.63         5.92        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        35.21         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-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E 
       12.16        44.75         3.68        47.38        23.18        25.22 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25         0.30        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V 
        1.38         3.16        29.00         7.13        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN 
        7.40        55.50         2.66        16.47        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
        8.71        13.41        52.57        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.15        12.59        13.25        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        12.85        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       13.18         0.13        12.03        12.85        12.26         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         8.98        25.81        27.09 
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        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6452 
        6.61        18.35         4.08         9.67         6.18        34.68 
TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
       17.29         9.17        40.21        30.90        21.90        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 
       28.73         3.45        29.56        14.43        11.44         8.05 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 
        2.66         2.20        15.58        31.10        26.33        14.79 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A452 
       25.18        12.79        27.12         7.53         8.22         7.53 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE 
       34.98        27.55         0.53        32.52        20.65        20.42 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 
       21.44        13.02        13.18        11.21        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 
       12.53         7.17        12.33        12.39        15.39        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 
       12.43        11.61        12.20         3.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-4477 
        8.05        19.07        12.03         0.00        12.00        30.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8570 
        1.02        12.03        15.02        18.54        15.98        24.72 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       20.91        16.44        14.76        11.24        20.32        22.29 
TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8211 
        0.62        21.27         3.48        14.07        22.29        13.58 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.56        26.47         5.92        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        25.81        11.77         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RN 
       29.00        23.84        21.17        33.40        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        6.44        10.62        11.70        63.62        45.67        18.21 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DT 
        6.08        16.67       115.69        35.61         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        5.46        13.02        18.48        43.36        21.73         7.73 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PX 
       16.31         2.70        17.85        23.41        13.35        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       73.41        21.83        20.81         9.73        55.56         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        66.81        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6J 
       18.41        43.66        38.93        32.94        54.12        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       34.85        18.28         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-KB-A93G 
        0.36        20.02        21.99        22.98        79.07        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IG-A4QT 
        9.86        26.93        25.78        13.94         8.94         9.30 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       14.86       122.10        68.02        41.52        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         6.28         3.16        26.33        32.61        21.01 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 
       58.59         4.90         7.43        25.12         3.75         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU 
       12.92        13.48        13.55         7.76        21.37        83.24 
TCGA-L5-A8NW TCGA-LN-A49U TCGA-LN-A49X TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 
       46.09        15.35        12.62        33.11         7.82        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.04        38.40         9.30        15.78         2.30         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29        16.44        15.35         1.55        46.19        18.21 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        2.10         2.66         9.47         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 
       30.90         4.08         9.34         9.57         6.61        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-6803 
       25.61        18.05        19.89        12.16         8.98        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       39.78        18.15         9.07        33.21        37.25         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       29.59         9.60        32.25         0.56        29.42        19.96 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
        1.12         9.34        28.14         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08         1.48        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.72        14.17        28.34         0.66        13.51         0.46 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
        1.15        16.14         5.13        13.41        13.15        13.35 
TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.76        12.30        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43         6.31        11.31         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       20.02        27.02         1.02        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 
       29.98         9.01        18.97         7.07         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        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        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        14.27         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        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 
       19.96         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-FP-A9TM 
       19.53        17.06        59.54         5.03         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
       77.29        63.06        52.21        30.51         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.30         5.59        22.68        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H8 
        6.51         6.58        20.25         0.26        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X 
       12.46         6.74        12.59         6.51        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04         8.52        74.53         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         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-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.25        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        22.19         2.50        12.79         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        29.59        14.33        39.45        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6D 
       55.43         6.58         2.66        11.24        28.41        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          0.0                           0.1 
  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 
                        13.22                         14.66 
[1] "0.0 - 115.7 (13.2)" "0.1 - 122.3 (14.7)"
[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       18       12        47
  AMP PEAK  6(3Q26.2) WILD-TYPE       7       12       29       21        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(3Q26.2) MUTATED          43        23         37         29
  AMP PEAK  6(3Q26.2) WILD-TYPE        44         5         58         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  6(3Q26.2) MUTATED           25       19         3
  AMP PEAK  6(3Q26.2) WILD-TYPE         21       30         1
D6V3, multiclass
            clus
vv           AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                             9                            12
  STAGE IB                            18                            29
  STAGE II                            12                            21
  STAGE IIA                           47                            40
  STAGE IIB                           43                            44
  STAGE III                           23                             5
  STAGE IIIA                          37                            58
  STAGE IIIB                          29                            43
  STAGE IIIC                          25                            21
  STAGE IV                            19                            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
  AMP PEAK  6(3Q26.2) MUTATED      24  64 127  57
  AMP PEAK  6(3Q26.2) WILD-TYPE    31  72 156  67
D6V4, multiclass
       clus
vv      AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  T0+T1                          24                            31
  T2                             64                            72
  T3                            127                           156
  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    95  91  41  41
  AMP PEAK  6(3Q26.2) WILD-TYPE 112  96  57  55
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  N0                          95                           112
  N1                          91                            96
  N2                          41                            57
  N3                          41                            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   236  16
  AMP PEAK  6(3Q26.2) WILD-TYPE 288  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED    236   16
  AMP PEAK  6(3Q26.2) WILD-TYPE  288   23
   clus
vv  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  0                         236                           288
  1                          16                            23
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED    74 213
  AMP PEAK  6(3Q26.2) WILD-TYPE 111 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED     74  213
  AMP PEAK  6(3Q26.2) WILD-TYPE  111  227
        clus
vv       AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  FEMALE                          74                           111
  MALE                           213                           227
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED   195  68
  AMP PEAK  6(3Q26.2) WILD-TYPE 250  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED    195   68
  AMP PEAK  6(3Q26.2) WILD-TYPE  250   51
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  NO                          195                           250
  YES                          68                            51
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(3Q26.2) MUTATED      79                        10
  AMP PEAK  6(3Q26.2) WILD-TYPE    55                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(3Q26.2) MUTATED                                           0   162
  AMP PEAK  6(3Q26.2) WILD-TYPE                                         1   230
D6V11, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q26.2) MUTATED
  ASIAN                                                              79
  BLACK OR AFRICAN AMERICAN                                          10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             162
                                           clus
vv                                          AMP PEAK  6(3Q26.2) WILD-TYPE
  ASIAN                                                                55
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     8 174
  AMP PEAK  6(3Q26.2) WILD-TYPE   3 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      8  174
  AMP PEAK  6(3Q26.2) WILD-TYPE    3  230
                        clus
vv                       AMP PEAK  6(3Q26.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         174
                        clus
vv                       AMP PEAK  6(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           230
[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   136  85
  AMP PEAK  7(5P15.33) WILD-TYPE 218 160
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           221                            378 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            85                            160 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG 
       18.28         4.31         8.94        19.99         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       27.12         5.16        47.05        22.98         0.23        20.15 
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        47.38        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR 
        3.16         0.30        32.61        47.93         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        4.90        29.00         7.13        15.48         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NV 
       55.50        12.92        16.47        13.55        13.41        52.57 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.85        10.36         5.92        13.41        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A4 
       15.35        13.25        12.62        12.46        12.59        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.18        12.33        13.38        13.18        12.85        12.26 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO 
        5.06        16.31        38.40        53.95        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU 
       20.38         3.42        16.44        25.81        27.09        18.31 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T6 
       33.70        18.18        52.27        18.05        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-BR-4187 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        4.64         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
        3.45        11.44         0.69         8.05        29.42         2.66 
TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 
       15.58         0.26        17.52        26.33        14.79         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 
       20.22        24.79         8.22        20.65        21.44        13.15 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 
       13.18        12.10        12.59        12.33        12.30        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 
       12.82         6.31        12.43        11.61        12.20         7.99 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       54.08        14.01        12.03        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5577 
       36.00         0.99        12.03        15.02         4.01        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       12.66        20.91        19.13        17.19        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 
       12.36        11.31        24.72        14.66        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       15.65        19.96         0.62         7.99        72.23         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
       19.53        17.06        77.29         1.51        18.15        28.96 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       24.30         3.25        22.75        25.81        11.77         6.58 
TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RR 
        2.10        23.80        33.40         3.45        13.35         6.74 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT 
       10.62         5.56        14.04        45.67        18.21         8.61 
TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV 
      122.30        57.44         8.94        35.61         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PH TCGA-VQ-A8PK 
       13.02        18.48        43.36        21.73        12.79        17.85 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       39.45        18.74         1.71        42.64         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        9.04         4.54         6.58        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       38.93        54.12        16.14        27.55         0.79 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        60.39        34.85        24.00         4.70        22.82 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU 
       20.02        21.99        79.07        16.24         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       26.93        25.78        31.27        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24         4.21         7.69        35.21         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-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       14.86        12.16       122.10        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
       24.03         6.28        30.25        26.33        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        3.32         1.38        58.59         7.43        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.02         2.66        13.48        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49M 
       21.37         8.71        83.24        46.09        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A9 
       12.43        12.33        12.59        12.49        12.76        11.54 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.03        33.11         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.04         6.35         9.30         2.89         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER 
        5.29        15.35         9.27         8.98        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
        1.55         8.12        28.11        46.19        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
       18.21        41.23        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 
       11.01         9.47         9.44         6.61         6.97         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-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-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       35.84        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       37.25        14.43        29.59         9.60        32.25         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20         7.40         6.18        31.10        13.08 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.02        13.35        11.21        12.76        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        11.64        12.07        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.31         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 
       27.02        15.95         1.02         8.05         4.01        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-5728 TCGA-CG-5732 
        0.99         6.02       105.07        28.96        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        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44        20.32         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27        11.38        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51        26.47         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       24.20        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         0.26        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       14.07        15.68        36.36        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       12.46        19.53         6.44        12.59         6.51        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       15.75        13.51         2.53        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05         5.13        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      115.69       116.38        71.38        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92        48.79        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        2.70         1.87         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        20.81        32.88        60.85         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        66.81        21.04         2.66        42.54 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        32.94        17.13        26.04        12.43        17.26 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.23                           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 
                         13.38                          14.12 
[1] "0.2 - 122.3 (13.4)" "0.0 - 122.1 (14.1)"
[1] "hr=" "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        41
  AMP PEAK  7(5P15.33) WILD-TYPE       9       15       31       22        46
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(5P15.33) MUTATED          29        13         38         20
  AMP PEAK  7(5P15.33) WILD-TYPE        58        15         57         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         31       30         3
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              6                             15
  STAGE IB                             16                             31
  STAGE II                             11                             22
  STAGE IIA                            41                             46
  STAGE IIB                            29                             58
  STAGE III                            13                             15
  STAGE IIIA                           38                             57
  STAGE IIIB                           20                             52
  STAGE IIIC                           15                             31
  STAGE IV                             19                             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
  AMP PEAK  7(5P15.33) MUTATED      12  53 127  26
  AMP PEAK  7(5P15.33) WILD-TYPE    43  83 156  98
D7V4, multiclass
       clus
vv      AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  T0+T1                           12                             43
  T2                              53                             83
  T3                             127                            156
  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    79  69  35  32
  AMP PEAK  7(5P15.33) WILD-TYPE 128 118  63  64
D7V5, multiclass
    clus
vv   AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  N0                           79                            128
  N1                           69                            118
  N2                           35                             63
  N3                           32                             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"
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   186  14
  AMP PEAK  7(5P15.33) WILD-TYPE 338  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    186   14
  AMP PEAK  7(5P15.33) WILD-TYPE  338   25
   clus
vv  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  0                          186                            338
  1                           14                             25
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED    55 173
  AMP PEAK  7(5P15.33) WILD-TYPE 130 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     55  173
  AMP PEAK  7(5P15.33) WILD-TYPE  130  267
        clus
vv       AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  FEMALE                           55                            130
  MALE                            173                            267
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED   157  50
  AMP PEAK  7(5P15.33) WILD-TYPE 288  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED    157   50
  AMP PEAK  7(5P15.33) WILD-TYPE  288   69
     clus
vv    AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  NO                           157                            288
  YES                           50                             69
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(5P15.33) MUTATED      60                         9
  AMP PEAK  7(5P15.33) WILD-TYPE    74                         8
                                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     133
  AMP PEAK  7(5P15.33) WILD-TYPE   259
D7V11, multiclass
                                           clus
vv                                          AMP PEAK  7(5P15.33) MUTATED
  ASIAN                                                               60
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              133
                                           clus
vv                                          AMP PEAK  7(5P15.33) WILD-TYPE
  ASIAN                                                                 74
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                259
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     3 141
  AMP PEAK  7(5P15.33) WILD-TYPE   8 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      3  141
  AMP PEAK  7(5P15.33) WILD-TYPE    8  263
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            263
[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   127  81
  AMP PEAK  8(5P13.1) WILD-TYPE 227 164
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                          208                           391 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                           81                           164 
$`AMP PEAK  8(5P13.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG 
       18.28         4.31         8.94        19.99         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX 
       27.12         5.16        47.05        21.99        22.98         0.23 
TCGA-KB-A93G TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
       20.15        14.30         5.92        16.24        32.45        33.27 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 
        0.85         2.63        20.12        18.64         0.53         0.79 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       23.41         4.67        14.50        44.75        68.02         3.68 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OM 
       47.38        31.56        25.22         3.16        32.61        47.93 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S 
        7.17         3.16         4.90        29.00         7.13        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NQ 
        2.60         3.75        55.50        12.92        13.55        21.37 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49O 
       13.41        52.57        46.09        10.85        10.36        13.41 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.38        13.25        12.62        12.59        12.59        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.33        13.22         4.47        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-RE-A7BO 
       12.85        12.26         5.06        16.31        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         8.98        27.09        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       52.27        18.05        15.91        25.08        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-4187 TCGA-BR-6458 
        2.10         1.32         2.66        19.73         4.64        19.33 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
        9.21        35.24        33.63        39.78        18.15         3.45 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 
       33.21        11.44         0.69         8.05        29.42         2.66 
TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8373 
       15.58         0.26        17.52        26.33        14.04        14.79 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4PD 
        9.21        20.22        24.79         8.22        34.98        20.65 
TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
       21.44        13.18        12.10        12.76        12.59        12.33 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4436 
       12.82         6.31        12.43        11.61        12.20         7.99 
TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       54.08        12.03        18.97         7.07        12.00        36.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 
        0.99        12.03        15.02         4.01        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       19.13        10.26        15.22        12.36        11.31        24.72 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       14.66        11.31        22.29        15.65         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8238 
       72.23         3.48        19.53        17.06        77.29         1.51 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD 
       18.15        28.96        22.82        24.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
       25.81        11.77         2.10        23.80        33.40         3.45 
TCGA-IN-A6RL TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F5 
       13.35         6.51        10.62        11.70        15.75         5.56 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
       14.04        45.67        18.21        57.44         8.94        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8PH 
        5.46        13.25        13.02        18.48        21.73        12.79 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       17.85        39.45        18.74         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
        9.04         6.58        11.24        43.66        38.93        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        27.55        12.43         0.79 

$`AMP PEAK  8(5P13.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        60.39        34.85        24.00         4.70        22.82 
TCGA-S8-A6BV TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       20.02        79.07        16.24         9.86        27.35        26.93 
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-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT 
        4.21         7.69        35.21        20.78         3.88         9.30 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6F8 
       17.03        12.82         9.96        14.86        12.16       122.10 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       41.52        21.70        23.18        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.30        26.33        21.01        18.35         3.32         1.38 
TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       58.59         7.43        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-A49P 
       83.24         5.92        10.45        12.66        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.59        12.46        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A9FO TCGA-LN-A9FP 
       22.39        15.52        11.54        10.52         0.13        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         8.02         7.59         7.04        38.40 
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         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ 
        5.29        16.44        15.35         9.27        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D 
       12.43         1.55        18.31         8.12        18.18        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-3M-AB46 TCGA-B7-5816 
       11.24         9.17        18.21        41.23        58.03        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-4253 TCGA-BR-4255 
        6.97         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       36.16        35.84        15.32        28.73         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       37.25        14.43        29.59         9.60        32.25         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20         7.40         6.18        31.10        13.08 
TCGA-BR-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        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 
        7.36        25.05         3.72         5.39        25.18         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       26.73        31.96        32.58         9.86        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       28.34         0.66        32.52        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       13.35        11.21        12.53         7.17        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 
       12.59        11.64        15.39        12.07        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.31         6.58        11.77        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-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
       29.98        19.07         0.00         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        1.02         0.99         6.02       105.07        28.96        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        25.71        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        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34        19.96         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       26.47         5.92        24.39        22.32        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        24.26        22.68        24.20        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.44         6.74        12.59        13.51         2.53        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-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-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-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        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        14.33        73.41        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 
       20.81        32.88         1.71        42.64        60.85         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        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       42.54        18.41        28.41        32.94        17.13        26.04 
TCGA-ZA-A8F6 
       17.26 

  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                         0.23                          0.00 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                        77.29                        122.30 
  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE 
                       13.365                        14.270 
[1] "0.2 - 77.3 (13.4)"  "0.0 - 122.3 (14.3)"
[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        35
  AMP PEAK  8(5P13.1) WILD-TYPE       9       14       31       23        52
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(5P13.1) MUTATED          29        11         33         19
  AMP PEAK  8(5P13.1) WILD-TYPE        58        17         62         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  8(5P13.1) MUTATED           17       18         2
  AMP PEAK  8(5P13.1) WILD-TYPE         29       31         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             7                            14
  STAGE IB                            16                            31
  STAGE II                            10                            23
  STAGE IIA                           35                            52
  STAGE IIB                           29                            58
  STAGE III                           11                            17
  STAGE IIIA                          33                            62
  STAGE IIIB                          19                            53
  STAGE IIIC                          17                            29
  STAGE IV                            18                            31
  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      12  50 112  32
  AMP PEAK  8(5P13.1) WILD-TYPE    43  86 171  92
D8V4, multiclass
       clus
vv      AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  T0+T1                          12                            43
  T2                             50                            86
  T3                            112                           171
  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    72  69  27  35
  AMP PEAK  8(5P13.1) WILD-TYPE 135 118  71  61
D8V5, multiclass
    clus
vv   AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  N0                          72                           135
  N1                          69                           118
  N2                          27                            71
  N3                          35                            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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED   173  15
  AMP PEAK  8(5P13.1) WILD-TYPE 351  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED    173   15
  AMP PEAK  8(5P13.1) WILD-TYPE  351   24
   clus
vv  AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  0                         173                           351
  1                          15                            24
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED    57 159
  AMP PEAK  8(5P13.1) WILD-TYPE 128 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED     57  159
  AMP PEAK  8(5P13.1) WILD-TYPE  128  281
        clus
vv       AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  FEMALE                          57                           128
  MALE                           159                           281
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED   154  40
  AMP PEAK  8(5P13.1) WILD-TYPE 291  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED    154   40
  AMP PEAK  8(5P13.1) WILD-TYPE  291   79
     clus
vv    AMP PEAK  8(5P13.1) MUTATED AMP PEAK  8(5P13.1) WILD-TYPE
  NO                          154                           291
  YES                          40                            79
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(5P13.1) MUTATED      49                         9
  AMP PEAK  8(5P13.1) WILD-TYPE    85                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(5P13.1) MUTATED                                           0   131
  AMP PEAK  8(5P13.1) WILD-TYPE                                         1   261
D8V11, multiclass
                                           clus
vv                                          AMP PEAK  8(5P13.1) MUTATED
  ASIAN                                                              49
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             131
                                           clus
vv                                          AMP PEAK  8(5P13.1) WILD-TYPE
  ASIAN                                                                85
  BLACK OR AFRICAN AMERICAN                                             8
  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"
D8V12, binary
                               cls
clus                              0   1
  AMP PEAK  8(5P13.1) MUTATED     3 132
  AMP PEAK  8(5P13.1) WILD-TYPE   8 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(5P13.1) MUTATED      3  132
  AMP PEAK  8(5P13.1) WILD-TYPE    8  272
                        clus
vv                       AMP PEAK  8(5P13.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         132
                        clus
vv                       AMP PEAK  8(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           272
[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  87
  AMP PEAK  9(6P21.1) WILD-TYPE 259 158
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                          182                           417 
  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                           87                           158 
$`AMP PEAK  9(6P21.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-5727 
       60.39         0.36        35.97        27.12        20.02        79.07 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       27.35        25.78        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-IG-A8O2 TCGA-IG-A97I 
        8.94        16.24         4.21         3.88         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OM 
      122.10        44.75        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        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
       13.48         5.49        21.37        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
        5.92        10.45        13.15        12.59        12.62        12.49 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 
       11.54        12.33        12.33        12.00        12.23        13.18 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.26         8.02         7.59        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8EQ 
       53.95        15.78         2.89         3.42         8.98        22.82 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-A5TJ 
       15.91        25.08         2.10         1.32        58.03        11.01 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 
        6.61         6.97        18.35         4.08         9.67         6.18 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
       17.29        13.68        19.33         9.17         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8286 
       33.63        18.15        28.73         3.45        11.44        29.42 
TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        2.66        14.04        14.79        25.18         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE 
       24.79         9.86        20.88        34.98        20.65        20.42 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       21.44        13.02        11.21        12.82         6.31        12.30 
TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       11.61         7.99        54.08        19.07        12.03        18.97 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6527 
       30.97        36.00         4.01        69.04        19.13        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
       15.22        15.98        12.36        11.31        12.33        14.66 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-7735 
       14.27        16.44        22.29        15.65         7.99         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HU-8243 
       19.53        17.06         0.56         5.52        52.21         5.92 
TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 
       28.96        25.81        23.84        23.80        21.17         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       18.38        13.35        19.53         6.74        12.59        10.62 
TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53        37.64        36.95        14.04        45.67        18.21 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        8.61       122.30        37.91       115.69         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        43.36         7.73        22.19         2.70        17.85 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D 
       32.88         1.71         9.50         9.04         4.54        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       21.04        42.54        18.41        43.66        32.94        17.13 
TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       26.04         0.79 

$`AMP PEAK  9(6P21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 
        4.70        19.99        22.82         5.16        47.05        21.99 
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U 
       22.98        16.24         0.23        20.15         9.86        26.93 
TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       31.27         5.92        32.45         7.69        33.27        35.21 
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-A97H TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
       14.86        14.50         3.68        41.52        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       31.56        25.22        24.03         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT 
       26.33        32.61        21.01         3.32         3.16         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NK 
       29.00         7.43        25.12         7.40        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-A49P TCGA-LN-A49R TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.25        12.46        12.59        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.85        15.52        13.22         4.47        25.25        10.52 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.85        33.11         7.82         5.06         6.35         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE 
        2.30        12.69         7.00        20.38         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       15.35         9.27        25.81        27.09        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        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 
       46.19        18.05        11.24         9.17        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       14.37         3.42         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       19.56         9.47         9.44         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-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        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        39.78        15.32 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       29.59         9.60        32.25         8.05         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        5.39         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 
        6.28         7.53        26.73        31.96        32.58         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.15        16.14         5.13        13.41        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
       12.07        12.43        11.31        12.43         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
        1.02         8.05         4.01        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01         7.07        12.00         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       65.10        21.07         7.99        25.71        12.66        20.91 
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-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       17.19        12.79        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        21.14        20.91         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27        11.38        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        5.03        13.58         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        12.95        29.00        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A7NR 
       36.36         3.45        18.81        12.46         6.44         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
       11.70        15.75        13.51         5.56        63.62         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       19.73         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13        16.67        40.64       116.38        71.38 
TCGA-RD-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-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        0.92        48.79        13.25        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        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-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        55.56         2.01        55.43         6.58         5.72 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
        2.66        11.24        28.41        38.93        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE 
                         0.36                          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 
                       14.155                        13.780 
[1] "0.4 - 122.3 (14.2)" "0.0 - 116.4 (13.8)"
[1] "hr=" "1.2"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6P21.1) MUTATED         6        6       17       11        25
  AMP PEAK  9(6P21.1) WILD-TYPE       4       15       30       22        62
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6P21.1) MUTATED          28        12         28         19
  AMP PEAK  9(6P21.1) WILD-TYPE        59        16         67         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK  9(6P21.1) MUTATED            7       12         3
  AMP PEAK  9(6P21.1) WILD-TYPE         39       37         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  STAGE I                              6                             4
  STAGE IA                             6                            15
  STAGE IB                            17                            30
  STAGE II                            11                            22
  STAGE IIA                           25                            62
  STAGE IIB                           28                            59
  STAGE III                           12                            16
  STAGE IIIA                          28                            67
  STAGE IIIB                          19                            53
  STAGE IIIC                           7                            39
  STAGE IV                            12                            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
  AMP PEAK  9(6P21.1) MUTATED      19  49  83  26
  AMP PEAK  9(6P21.1) WILD-TYPE    36  87 200  98
D9V4, multiclass
       clus
vv      AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  T0+T1                          19                            36
  T2                             49                            87
  T3                             83                           200
  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    64  65  29  20
  AMP PEAK  9(6P21.1) WILD-TYPE 143 122  69  76
D9V5, multiclass
    clus
vv   AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  N0                          64                           143
  N1                          65                           122
  N2                          29                            69
  N3                          20                            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   154   9
  AMP PEAK  9(6P21.1) WILD-TYPE 370  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED    154    9
  AMP PEAK  9(6P21.1) WILD-TYPE  370   30
   clus
vv  AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  0                         154                           370
  1                           9                            30
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED    48 144
  AMP PEAK  9(6P21.1) WILD-TYPE 137 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED     48  144
  AMP PEAK  9(6P21.1) WILD-TYPE  137  296
        clus
vv       AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  FEMALE                          48                           137
  MALE                           144                           296
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED   136  38
  AMP PEAK  9(6P21.1) WILD-TYPE 309  81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED    136   38
  AMP PEAK  9(6P21.1) WILD-TYPE  309   81
     clus
vv    AMP PEAK  9(6P21.1) MUTATED AMP PEAK  9(6P21.1) WILD-TYPE
  NO                          136                           309
  YES                          38                            81
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(6P21.1) MUTATED      34                         8
  AMP PEAK  9(6P21.1) WILD-TYPE   100                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(6P21.1) MUTATED                                           1   124
  AMP PEAK  9(6P21.1) WILD-TYPE                                         0   268
D9V11, multiclass
                                           clus
vv                                          AMP PEAK  9(6P21.1) MUTATED
  ASIAN                                                              34
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             124
                                           clus
vv                                          AMP PEAK  9(6P21.1) WILD-TYPE
  ASIAN                                                               100
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D9V12, binary
                               cls
clus                              0   1
  AMP PEAK  9(6P21.1) MUTATED     3 116
  AMP PEAK  9(6P21.1) WILD-TYPE   8 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6P21.1) MUTATED      3  116
  AMP PEAK  9(6P21.1) WILD-TYPE    8  288
                        clus
vv                       AMP PEAK  9(6P21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         116
                        clus
vv                       AMP PEAK  9(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           288
[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    66  68
  AMP PEAK 10(6Q12) WILD-TYPE 288 177
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                        134                         465 
  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                         68                         177 
$`AMP PEAK 10(6Q12) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A8NT TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GK 
       60.39         8.94        27.12         9.86        25.78         7.63 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A97H 
       13.94        16.24         4.21         0.85         3.88        14.50 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OW 
       68.02         3.68        30.25        47.93        18.35         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        7.43        15.48         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
       13.48         5.49        21.37        52.57        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A4A9 TCGA-LN-A4MQ 
        5.92        10.45        13.15        13.25        11.54        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-M9-A5M8 
        4.47        12.33        12.00        12.23        13.18        33.11 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
        8.02        16.31         7.04        38.40        53.95        15.78 
TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-AA7I TCGA-Z6-A8JE 
        2.89        20.38        22.82        18.18        15.91         2.10 
TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4257 
       58.03        11.01         6.61         6.97         4.08         9.67 
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        33.63 
TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 
       28.73        11.44        29.42         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        24.79        20.88         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5804 TCGA-CD-8533 
       20.65        20.42        21.44        13.02        12.10        15.39 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        6.31        12.30        12.43         7.99        54.08         4.01 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5730 TCGA-D7-6526 TCGA-D7-6527 
       18.97        30.97         1.02         4.01        17.19        10.26 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6F0 
       12.36        11.31        12.33        14.66        14.27        22.29 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HU-A4GF 
        7.99         3.48        19.53         5.52        52.21        25.81 
TCGA-HU-A4GT TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-KB-A6F7 
        6.51        21.17         3.39        18.38        13.35        63.62 
TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
       37.64        14.04         8.61        37.91       115.69         8.94 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.25        13.02         7.73        22.19         2.70        17.85 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94R TCGA-VQ-AA68 
       32.88         1.71         9.50         9.04        42.54        43.66 
TCGA-VQ-AA6B TCGA-VQ-AA6F 
       32.94        54.12 

$`AMP PEAK 10(6Q12) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        35.97         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15        27.35        26.93        31.27        14.30        58.55 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
        5.92         8.94        32.45         7.69        33.27        35.21 
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-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-A6F8 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67        12.16       122.10        44.75        41.52        47.38 
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-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        3.16         0.30        26.33        32.61        21.01         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60        25.12         7.40        55.50        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-A49P TCGA-LN-A49R TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        22.39        12.85        15.52        13.22        25.25 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO 
       10.52        12.03        13.18        12.33        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        12.85        12.26         7.82         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
        6.35         9.30         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.21        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.66        19.73        26.70        11.70        19.56         9.47 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72         5.39        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       26.73        31.96        32.58         9.86         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       34.13        13.87         7.53         6.08        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL 
       28.34         0.66        32.52         0.46         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.15        13.18        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
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        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
        7.07        12.00         6.97        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 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        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-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-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
       13.58         0.56         6.21        77.29        63.06        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        19.53         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 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24        11.05         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        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-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74        20.81        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        55.56         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-AA64 
        5.72        66.81        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        38.93        17.13        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE 
                       0.72                        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 
                     13.215                      14.330 
[1] "0.7 - 115.7 (13.2)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D10V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(6Q12) MUTATED         4        3       14        6        21
  AMP PEAK 10(6Q12) WILD-TYPE       6       18       33       27        66
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(6Q12) MUTATED          18        10         17         13
  AMP PEAK 10(6Q12) WILD-TYPE        69        18         78         59
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(6Q12) MUTATED            6       12         3
  AMP PEAK 10(6Q12) WILD-TYPE         40       37         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  STAGE I                            4                           6
  STAGE IA                           3                          18
  STAGE IB                          14                          33
  STAGE II                           6                          27
  STAGE IIA                         21                          66
  STAGE IIB                         18                          69
  STAGE III                         10                          18
  STAGE IIIA                        17                          78
  STAGE IIIB                        13                          59
  STAGE IIIC                         6                          40
  STAGE IV                          12                          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
  AMP PEAK 10(6Q12) MUTATED      12  32  67  21
  AMP PEAK 10(6Q12) WILD-TYPE    43 104 216 103
D10V4, multiclass
       clus
vv      AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  T0+T1                        12                          43
  T2                           32                         104
  T3                           67                         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
  AMP PEAK 10(6Q12) MUTATED    50  45  16  18
  AMP PEAK 10(6Q12) WILD-TYPE 157 142  82  78
D10V5, multiclass
    clus
vv   AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  N0                        50                         157
  N1                        45                         142
  N2                        16                          82
  N3                        18                          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"
D10V6, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED   111  11
  AMP PEAK 10(6Q12) WILD-TYPE 413  28
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED    111   11
  AMP PEAK 10(6Q12) WILD-TYPE  413   28
   clus
vv  AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  0                       111                         413
  1                        11                          28
[1] 2 2
[1] FALSE
D10V7, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED    38 103
  AMP PEAK 10(6Q12) WILD-TYPE 147 337
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED     38  103
  AMP PEAK 10(6Q12) WILD-TYPE  147  337
        clus
vv       AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  FEMALE                        38                         147
  MALE                         103                         337
[1] 2 2
[1] FALSE
D10V8, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED    99  28
  AMP PEAK 10(6Q12) WILD-TYPE 346  91
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED     99   28
  AMP PEAK 10(6Q12) WILD-TYPE  346   91
     clus
vv    AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  NO                         99                         346
  YES                        28                          91
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(6Q12) MUTATED      27                         4
  AMP PEAK 10(6Q12) WILD-TYPE   107                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(6Q12) MUTATED                                           1    88
  AMP PEAK 10(6Q12) WILD-TYPE                                         0   304
D10V11, multiclass
                                           clus
vv                                          AMP PEAK 10(6Q12) MUTATED
  ASIAN                                                            27
  BLACK OR AFRICAN AMERICAN                                         4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            88
                                           clus
vv                                          AMP PEAK 10(6Q12) WILD-TYPE
  ASIAN                                                             107
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             304
[1] 4 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, binary
                             cls
clus                            0   1
  AMP PEAK 10(6Q12) MUTATED     1  85
  AMP PEAK 10(6Q12) WILD-TYPE  10 319
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 10(6Q12) MUTATED      1   85
  AMP PEAK 10(6Q12) WILD-TYPE   10  319
                        clus
vv                       AMP PEAK 10(6Q12) MUTATED AMP PEAK 10(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        85                         319
[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    51  56
  AMP PEAK 11(6Q21) WILD-TYPE 303 189
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                        107                         492 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         56                         189 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-L5-A43I TCGA-L5-A4OG TCGA-L5-A8NT TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 
       18.28         4.70        27.12        47.05        16.24         9.86 
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-A4OX TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43        15.48         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NQ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       12.92        13.48        21.37        10.85        10.36        10.45 
TCGA-LN-A5U5 TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-A8EZ 
        4.47         8.02        16.31         7.04        15.78        18.18 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 
       11.24        15.91        11.01         6.61         6.97         4.08 
TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
        9.67        17.29         9.21        35.24        33.63        18.15 
TCGA-BR-8060 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8485 
       11.44         2.66        14.04        14.79        25.18         9.21 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       24.79        20.88         7.53        34.98         1.48         0.72 
TCGA-BR-A4J7 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A48A 
       32.52        13.02        13.15        12.33        12.30        12.43 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4477 
        3.02         7.99        54.08         4.01        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        12.36        11.31 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-A4GH TCGA-HU-A4GT 
       12.33        14.27         7.99         5.52        11.77         6.51 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A7NU 
       12.95        21.17         3.45        18.81         3.39        11.70 
TCGA-KB-A6F5 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW 
        5.56        14.04        45.67         8.61        16.67        37.91 
TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        8.94         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       22.19         2.70        17.85        32.88         1.71         9.50 
TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-VQ-AA6J 
        9.04        66.81        42.54        17.13        27.55 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        35.97         5.16        20.02 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07         0.23        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN 
       26.93        25.78        31.27        58.55         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       16.24         4.21        32.45         7.69        33.27        35.21 
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-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
        3.68        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        2.60        25.12         7.40        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49         8.71        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       46.09         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
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-A5U6 
       12.85        15.52        11.54        12.33        13.22        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-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.26        33.11         7.82         7.59         5.06        38.40 
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         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        7.00        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       46.19        18.05         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-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-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-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        31.27         7.36        25.05         3.72         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-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-5801 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.82        12.43         6.31        11.31        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         8.05        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-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 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        15.98        12.79 
TCGA-D7-8570 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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RJ 
       14.07        15.68        33.40        36.36        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       13.35        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
       10.62        15.75        13.51         2.53        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95         3.72        19.73        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-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-A8E3 
       16.87        19.04         5.79         0.92        48.79        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-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        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81        42.64        60.85         9.73        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       54.12        26.04        16.14        12.43        17.26         0.79 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       0.72                        0.00 
  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 
                      12.92                       14.45 
[1] "0.7 - 68.0 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.6"
D11V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(6Q21) MUTATED         3        1       10        5         8
  AMP PEAK 11(6Q21) WILD-TYPE       7       20       37       28        79
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(6Q21) MUTATED          13         4         22         13
  AMP PEAK 11(6Q21) WILD-TYPE        74        24         73         59
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(6Q21) MUTATED            5       15         2
  AMP PEAK 11(6Q21) WILD-TYPE         41       34         2
D11V3, multiclass
            clus
vv           AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  STAGE I                            3                           7
  STAGE IA                           1                          20
  STAGE IB                          10                          37
  STAGE II                           5                          28
  STAGE IIA                          8                          79
  STAGE IIB                         13                          74
  STAGE III                          4                          24
  STAGE IIIA                        22                          73
  STAGE IIIB                        13                          59
  STAGE IIIC                         5                          41
  STAGE IV                          15                          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
  AMP PEAK 11(6Q21) MUTATED       7  25  47  26
  AMP PEAK 11(6Q21) WILD-TYPE    48 111 236  98
D11V4, multiclass
       clus
vv      AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1                         7                          48
  T2                           25                         111
  T3                           47                         236
  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  36  19  19
  AMP PEAK 11(6Q21) WILD-TYPE 178 151  79  77
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        29                         178
  N1                        36                         151
  N2                        19                          79
  N3                        19                          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"
D11V6, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    87  13
  AMP PEAK 11(6Q21) WILD-TYPE 437  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     87   13
  AMP PEAK 11(6Q21) WILD-TYPE  437   26
   clus
vv  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  0                        87                         437
  1                        13                          26
[1] 2 2
[1] FALSE
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    29  82
  AMP PEAK 11(6Q21) WILD-TYPE 156 358
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     29   82
  AMP PEAK 11(6Q21) WILD-TYPE  156  358
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                        29                         156
  MALE                          82                         358
[1] 2 2
[1] FALSE
D11V8, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    82  20
  AMP PEAK 11(6Q21) WILD-TYPE 363  99
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     82   20
  AMP PEAK 11(6Q21) WILD-TYPE  363   99
     clus
vv    AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  NO                         82                         363
  YES                        20                          99
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(6Q21) MUTATED      18                         5
  AMP PEAK 11(6Q21) WILD-TYPE   116                        12
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(6Q21) MUTATED                                           1    71
  AMP PEAK 11(6Q21) WILD-TYPE                                         0   321
D11V11, multiclass
                                           clus
vv                                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                                            18
  BLACK OR AFRICAN AMERICAN                                         5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            71
                                           clus
vv                                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                                             116
  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"
D11V12, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     1  64
  AMP PEAK 11(6Q21) WILD-TYPE  10 340
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      1   64
  AMP PEAK 11(6Q21) WILD-TYPE   10  340
                        clus
vv                       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                          10
  NOT HISPANIC OR LATINO                        64                         340
[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   200 138
  AMP PEAK 12(7P22.3) WILD-TYPE 154 107
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          338                           261 
  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE 
                          138                           107 
$`AMP PEAK 12(7P22.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX 
        0.36        35.97        27.12        21.99        22.98         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK 
       20.15         9.86        27.35        26.93        25.78         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94         8.94        16.24        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L 
       33.27        35.21         0.85        20.12        18.64         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 
       17.03         0.79        23.41         4.67        14.50       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        47.38        21.70        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       25.22         3.16        30.25         0.30        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS 
       47.93        18.35         3.32         1.38         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        4.90        29.00         7.13        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         5.49         8.71        13.41        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       10.85        10.36         5.92        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 
       13.15        15.35        13.25        12.62        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 
       12.76        12.59        12.85        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       25.25        10.52        12.00        12.03        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40        53.95         9.30 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET 
       15.35         9.27         8.98        25.81        22.82         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
       18.31         8.12        28.11        18.18        52.27        46.19 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       11.24        15.91        18.21        25.08        14.37         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 
        1.32         2.66        19.73        11.70        11.01         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 
        6.97         4.64        18.35         9.67        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 
        9.17        32.78        25.61        18.05        40.21         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
       36.16        35.24        33.63        39.78        18.15         3.45 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 
       29.56        33.21        14.43        11.44         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 
       31.10        13.08        22.19         0.95         3.32        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 
        7.36         5.39         9.21        20.22         1.12        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
        9.86         8.22        10.68        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 
        1.48        12.89         0.72         0.53        32.52        13.51 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 
       20.42         1.15        21.44        13.02        13.18        12.10 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.33        12.39        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        11.31        12.43        11.61         6.58        12.20 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01        14.01        19.07        18.97         7.07        12.00 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       36.00        12.03        28.96         4.01        21.07         7.99 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       12.66        20.91        19.13        18.84        18.54        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.36        11.31        12.33        24.72 
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-A6F0 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       16.44        36.43        22.29        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF 
       19.53        14.07        22.29        17.06         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 
        6.21        52.21        26.47        18.15        28.96        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58        20.25         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       21.17        33.40         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 
       13.35         6.44         6.51        11.70         5.56        63.62 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       37.64        45.67        18.21         8.52        74.53         6.08 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT 
        8.61       122.30        57.44         8.94         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
        7.73        34.29        46.26         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       17.85        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       18.74        20.81         1.71        60.85         9.50         2.01 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        4.54        66.81        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       43.66        38.93        32.94        54.12        16.14        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 12(7P22.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU TCGA-S8-A6BV 
       15.68        34.85        19.99        22.82         5.16        20.02 
TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       47.05        79.07        16.24        31.27        14.30        58.55 
TCGA-2H-A9GQ TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A625 
        4.21        20.78         2.63         3.88         9.30        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A6FG TCGA-JY-A93D TCGA-JY-A93F 
        9.96        14.86        12.16        41.52        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        6.28        21.01         7.17         7.43        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M 
       13.48         7.76        21.37        83.24        10.45        12.66 
TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.33        12.59        12.46        22.39        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 
        4.47        12.23        13.18        13.38        12.03        33.11 
TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8ER 
        6.35        15.78         2.89        16.44        27.09        12.43 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-3M-AB46 
       33.70        18.05         9.17        41.23         3.42        58.03 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4201 
       26.70        19.56         9.47         9.44         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
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        44.94 
TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 
       21.90        35.84        15.32        28.73         9.07        37.25 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8291 TCGA-BR-8363 
        0.69        29.59         9.60        32.25        19.96         0.26 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
       17.52        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         3.72        25.18        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       20.88        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
       14.17        28.34         0.66         0.46        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13        13.41        13.15        13.35        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.59        12.53         7.17        12.30        12.59        11.64 
TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4443 
       12.30        11.77        12.62         3.02         1.02        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        15.02        65.10 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       69.04        25.71        20.55        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A4YY 
       10.26        12.79        16.80        19.50         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        7.99        21.27        11.38        59.54         5.03        13.58 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        30.51         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY 
       22.68        24.20        21.37        29.98         6.51         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN 
       29.00        14.07        15.68        36.36        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59        10.62        15.75        13.51         2.53 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 TCGA-R5-A805 
       36.95         3.72        19.73        14.04         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-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
      116.38        71.38        35.61        16.87        19.04         0.92 
TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PE 
       18.48        38.14        37.22        30.97        16.31        22.19 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z 
       64.57        61.22        32.88        42.64         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 
        9.04        55.43         6.58         5.72         2.66        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J 
       17.13        26.04        27.55 

  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 
                       13.395                        14.760 
[1] "0.1 - 122.3 (13.4)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(7P22.3) MUTATED         8       10       24       15        46
  AMP PEAK 12(7P22.3) WILD-TYPE       2       11       23       18        41
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(7P22.3) MUTATED          51        22         52         35
  AMP PEAK 12(7P22.3) WILD-TYPE        36         6         43         37
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(7P22.3) MUTATED           28       25         3
  AMP PEAK 12(7P22.3) WILD-TYPE         18       24         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  STAGE I                              8                             2
  STAGE IA                            10                            11
  STAGE IB                            24                            23
  STAGE II                            15                            18
  STAGE IIA                           46                            41
  STAGE IIB                           51                            36
  STAGE III                           22                             6
  STAGE IIIA                          52                            43
  STAGE IIIB                          35                            37
  STAGE IIIC                          28                            18
  STAGE IV                            25                            24
  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      36  68 167  59
  AMP PEAK 12(7P22.3) WILD-TYPE    19  68 116  65
D12V4, multiclass
       clus
vv      AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  T0+T1                          36                            19
  T2                             68                            68
  T3                            167                           116
  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   111 109  56  52
  AMP PEAK 12(7P22.3) WILD-TYPE  96  78  42  44
D12V5, multiclass
    clus
vv   AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  N0                         111                            96
  N1                         109                            78
  N2                          56                            42
  N3                          52                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED   287  21
  AMP PEAK 12(7P22.3) WILD-TYPE 237  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED    287   21
  AMP PEAK 12(7P22.3) WILD-TYPE  237   18
   clus
vv  AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  0                         287                           237
  1                          21                            18
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED    84 269
  AMP PEAK 12(7P22.3) WILD-TYPE 101 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED     84  269
  AMP PEAK 12(7P22.3) WILD-TYPE  101  171
        clus
vv       AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  FEMALE                          84                           101
  MALE                           269                           171
[1] 2 2
[1] FALSE
D12V8, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED   252  63
  AMP PEAK 12(7P22.3) WILD-TYPE 193  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED    252   63
  AMP PEAK 12(7P22.3) WILD-TYPE  193   56
     clus
vv    AMP PEAK 12(7P22.3) MUTATED AMP PEAK 12(7P22.3) WILD-TYPE
  NO                          252                           193
  YES                          63                            56
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(7P22.3) MUTATED      76                        12
  AMP PEAK 12(7P22.3) WILD-TYPE    58                         5
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(7P22.3) MUTATED                                           1   219
  AMP PEAK 12(7P22.3) WILD-TYPE                                         0   173
D12V11, multiclass
                                           clus
vv                                          AMP PEAK 12(7P22.3) MUTATED
  ASIAN                                                              76
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             219
                                           clus
vv                                          AMP PEAK 12(7P22.3) WILD-TYPE
  ASIAN                                                                58
  BLACK OR AFRICAN AMERICAN                                             5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                               cls
clus                              0   1
  AMP PEAK 12(7P22.3) MUTATED     8 212
  AMP PEAK 12(7P22.3) WILD-TYPE   3 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(7P22.3) MUTATED      8  212
  AMP PEAK 12(7P22.3) WILD-TYPE    3  192
                        clus
vv                       AMP PEAK 12(7P22.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         212
                        clus
vv                       AMP PEAK 12(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           192
[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   191 134
  AMP PEAK 13(7P11.2) WILD-TYPE 163 111
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          325                           274 
  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          134                           111 
$`AMP PEAK 13(7P11.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       60.39        18.28         4.31        24.00         4.70        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 
        0.36        35.97        27.12         5.16        20.02        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        79.07         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN 
       26.93        25.78         7.63         5.92        13.94         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YC 
       16.24        32.45         7.69        35.21         0.85        20.12 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       18.64         0.53        17.03         0.79        23.41        14.50 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C 
       44.75        68.02        21.70        23.18        25.22         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       18.35         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 
       29.00         7.13        15.48         2.60         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        5.49         8.71        13.41        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
       10.36         5.92        13.41        13.38        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        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        12.85        15.52        12.33        13.22        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       25.25        12.00        12.03        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.06        16.31         7.04        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         7.00        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
       15.35         9.27         8.98        25.81        27.09         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        8.12        28.11        33.70        18.18        52.27        46.19 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       15.91        18.21        25.08        14.37         1.32         2.66 
TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.73        11.70        11.01         6.61         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 
       18.35         9.67        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        40.21         9.21        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       33.63        18.15         3.45        29.56        33.21        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         7.36 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
        5.39        20.22         1.12        32.58         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        34.98         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        32.52        13.51        20.42        21.44 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8530 
       13.02        13.18        12.10        12.53        12.33        12.39 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C 
       15.39        12.07        12.82        12.43         6.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        6.58        12.20        20.02        27.02        15.95         7.99 
TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 
        4.01        18.97         7.07        12.00        36.00        12.03 
TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       28.96        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       18.84        18.54        17.19        15.22        15.98        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       20.91        16.44        36.43        11.31        22.29        15.65 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       14.47        72.23         3.48        19.53        14.07        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 
        0.56         5.52         6.21        52.21        26.47         5.92 
TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       28.96        24.30        24.26         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         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       29.00        23.84        33.40         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        13.35         6.44         6.74        12.59         6.51 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZF 
       11.70         5.56        63.62        37.64        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       74.53         6.08         8.61        16.67       122.30       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PB TCGA-VQ-A8PF 
       18.48        43.36        21.73        37.41        34.29         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       12.79         2.70        17.85         1.87        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       39.45        11.70        21.83        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54        21.04        42.54        11.24        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

$`AMP PEAK 13(7P11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OI TCGA-CG-4444 TCGA-EQ-A4SO 
       15.68        34.85         8.94        19.99        47.05        16.24 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3YA 
       31.27        14.30        58.55         4.21        33.27        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-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67        12.16       122.10         3.68        41.52        47.38 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W 
       31.56        24.03         6.28         7.17         7.43        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-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A4A5 TCGA-LN-A4A9 
       12.66        12.43        12.33        13.15        22.39        11.54 
TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-M9-A5M8 
        4.47        10.52        12.23        13.18        13.38        33.11 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8ER 
       38.40         6.35        15.78        16.44        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A8JD 
       18.31        18.05        11.24         9.17        41.23         3.42 
TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        2.10        58.03        26.70        19.56         9.47         9.44 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        7.43        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       39.12        26.10        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       31.20        44.94        21.90        35.84        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       28.73         9.07        37.25        11.44        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 
       32.25        29.42         2.66        19.96         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
        0.26        22.19        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 
       31.27        25.05         3.72        25.18         9.21        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
       24.79        31.96        20.88        34.13         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
       27.55        28.57         8.98        28.34         0.66         0.46 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       20.65         1.15        16.14         5.13        13.41        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
       13.35        11.21        12.76        12.59         7.17        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI 
       12.59        11.64        12.30        11.31        12.43        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       12.62         3.02         1.02         8.05        54.08        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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 
       15.02        65.10         4.01        69.04        25.71        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 
       18.61        17.85        13.35        10.26        12.79        12.36 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       16.80        19.50        14.27         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        11.44        20.32         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         7.13         0.62         7.99        21.27        11.38 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 
       22.29        59.54         5.03        13.58        77.29        63.06 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       30.51         1.51        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       21.07         0.76         5.59        22.68        24.20        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 
       21.37        29.98         6.51         0.26        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NT 
       14.07        15.68        36.36        12.46        19.53        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       15.75        13.51         2.53        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
       14.04        45.67         4.60         9.24        11.05         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       37.91        40.64       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       19.04         5.79         0.92        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        46.26        16.31        22.19         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91S 
       15.65        13.35        29.59        64.57        61.22        32.88 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        9.73        55.43         6.58         5.72        66.81         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        28.41        17.13        26.04 

  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE 
                          0.1                           0.0 
  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 
                        13.41                         14.17 
[1] "0.1 - 122.3 (13.4)" "0.0 - 122.1 (14.2)"
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(7P11.2) MUTATED         8       11       24       13        44
  AMP PEAK 13(7P11.2) WILD-TYPE       2       10       23       20        43
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(7P11.2) MUTATED          49        20         51         37
  AMP PEAK 13(7P11.2) WILD-TYPE        38         8         44         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(7P11.2) MUTATED           26       21         3
  AMP PEAK 13(7P11.2) WILD-TYPE         20       28         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  STAGE I                              8                             2
  STAGE IA                            11                            10
  STAGE IB                            24                            23
  STAGE II                            13                            20
  STAGE IIA                           44                            43
  STAGE IIB                           49                            38
  STAGE III                           20                             8
  STAGE IIIA                          51                            44
  STAGE IIIB                          37                            35
  STAGE IIIC                          26                            20
  STAGE IV                            21                            28
  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      36  61 162  58
  AMP PEAK 13(7P11.2) WILD-TYPE    19  75 121  66
D13V4, multiclass
       clus
vv      AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  T0+T1                          36                            19
  T2                             61                            75
  T3                            162                           121
  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   111 103  52  49
  AMP PEAK 13(7P11.2) WILD-TYPE  96  84  46  47
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  N0                         111                            96
  N1                         103                            84
  N2                          52                            46
  N3                          49                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED   279  16
  AMP PEAK 13(7P11.2) WILD-TYPE 245  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED    279   16
  AMP PEAK 13(7P11.2) WILD-TYPE  245   23
   clus
vv  AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  0                         279                           245
  1                          16                            23
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED    84 255
  AMP PEAK 13(7P11.2) WILD-TYPE 101 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED     84  255
  AMP PEAK 13(7P11.2) WILD-TYPE  101  185
        clus
vv       AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  FEMALE                          84                           101
  MALE                           255                           185
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED   244  60
  AMP PEAK 13(7P11.2) WILD-TYPE 201  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED    244   60
  AMP PEAK 13(7P11.2) WILD-TYPE  201   59
     clus
vv    AMP PEAK 13(7P11.2) MUTATED AMP PEAK 13(7P11.2) WILD-TYPE
  NO                          244                           201
  YES                          60                            59
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(7P11.2) MUTATED      74                        14
  AMP PEAK 13(7P11.2) WILD-TYPE    60                         3
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(7P11.2) MUTATED                                           1   208
  AMP PEAK 13(7P11.2) WILD-TYPE                                         0   184
D13V11, multiclass
                                           clus
vv                                          AMP PEAK 13(7P11.2) MUTATED
  ASIAN                                                              74
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             208
                                           clus
vv                                          AMP PEAK 13(7P11.2) WILD-TYPE
  ASIAN                                                                60
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P11.2) MUTATED     6 205
  AMP PEAK 13(7P11.2) WILD-TYPE   5 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P11.2) MUTATED      6  205
  AMP PEAK 13(7P11.2) WILD-TYPE    5  199
                        clus
vv                       AMP PEAK 13(7P11.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         205
                        clus
vv                       AMP PEAK 13(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           199
[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   182 121
  AMP PEAK 14(7Q21.2) WILD-TYPE 172 124
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          303                           296 
  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE 
                          121                           124 
$`AMP PEAK 14(7Q21.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39        18.28        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       27.12        22.98        79.07         0.23        20.15         9.86 
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        35.21 
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-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 
       14.50        44.75        68.02         3.68        47.38        21.70 
TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H 
       23.18        31.56        25.22         3.16        30.25         0.30 
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        15.48         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.75         3.02         2.66        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.22        13.41        52.57        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59        12.85        15.52        11.54        12.33 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33        25.25        12.00        12.03        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 
        0.13        12.85         7.82         8.02         7.59         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
       38.40         6.35         9.30         2.89        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO 
       20.38         5.29         3.42        15.35         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TI 
       25.08         2.10         1.32        19.73        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4257 
       11.01         9.44         6.97         4.64        18.35         9.67 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       17.29        19.33        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       18.05        40.21         9.21        36.16        35.24        33.63 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8284 TCGA-BR-8285 
       29.56        33.21        14.43        11.44         8.05         0.56 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8366 
        2.20        15.58         7.40        13.08        17.52         0.95 
TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        3.32        14.79         7.36         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY 
        1.12        32.58         9.86        10.68        13.87        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.72        14.17         0.53        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 
        1.15        13.02        13.18        12.10         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.30        12.39        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 
        6.31        12.43        11.61         6.58        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         7.99        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       14.01        12.03        18.97         7.07        12.00        36.00 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 
       12.03        15.02        28.96        21.07        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       19.13        18.84        18.54        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       15.22        15.98        12.79        24.72        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV 
       14.66        21.14        20.91        16.44        36.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
       11.31        22.29        15.65        14.47        72.23         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7134 
       19.53        22.29        17.06         0.56         6.21        52.21 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
       26.47         5.92        28.96        24.30        24.26        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.58        20.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR 
       29.00         3.45         3.39        13.35         6.44         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       10.62        11.70         5.56        63.62         8.52        74.53 
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        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       37.41         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        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         2.01         4.54        66.81        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        38.93        32.94        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

$`AMP PEAK 14(7Q21.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85         4.31         8.94        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A8PU 
        5.16        20.02        47.05        21.99        16.24        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        25.78        14.30        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 
       13.94         4.21        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-A93F TCGA-KH-A6WC TCGA-L5-A4OF 
       12.16       122.10        41.52        24.03         6.28        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE 
       21.01         7.17         7.43        25.12         7.40        55.50 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.48         7.76         5.49        21.37         8.71        83.24 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.66        12.43        13.25        22.39        13.22         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR 
       10.52        12.23        13.18        13.38        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC 
       33.11         5.06        16.31        53.95        15.78         2.30 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I 
       16.44         8.98        22.82        12.43        52.27        15.91 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
       41.23        14.37         3.42         2.66        58.03        26.70 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        9.47         6.61         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       13.87        13.68        39.12        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7716 
       30.90        31.20        44.94        21.90        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 
       18.15        15.32        28.73         3.45         9.07        37.25 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 
        0.69        29.59         9.60        32.25        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8367 
       19.96         6.18        31.10         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        31.27        25.05         3.72 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        7.53        26.73        24.79        31.96        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       28.57         8.98        28.34         0.66        32.52         0.46 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       21.44        16.14         5.13        13.41        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8532 
       11.21        12.76        12.59        12.53        12.59        11.64 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 
       12.30        11.31        11.77        12.62         1.02         8.05 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
       29.98        19.07         0.00         9.01        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 
        1.02         0.99         6.02         0.99       105.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 
        4.01        69.04         7.99        25.71        20.55        18.61 
TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 
       17.85        12.36        11.31        12.33        16.80        18.21 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
       14.27         5.92        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       20.32         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 
        7.99        21.27        11.38        14.07        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 
       13.58         5.52        77.29        63.06        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
        5.59        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.37        29.98         6.51         0.26        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       21.17        14.07        15.68        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-AB1V 
       18.38        12.46        19.53         6.74        12.59        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         2.53        37.64        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       14.04        45.67        18.21         4.60         9.24        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
        5.13        16.67        40.64       116.38        71.38        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.87        19.04         5.79         0.92         5.46        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14        37.22        30.97        46.26        16.31        22.19 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
       61.22        18.74         9.73        55.56         9.04        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        6.58         5.72         2.66        43.66        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 
                          0.1                           0.0 
  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 
                       13.380                        14.285 
[1] "0.1 - 122.3 (13.4)" "0.0 - 122.1 (14.3)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(7Q21.2) MUTATED         6        9       23       16        47
  AMP PEAK 14(7Q21.2) WILD-TYPE       4       12       24       17        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(7Q21.2) MUTATED          42        14         43         38
  AMP PEAK 14(7Q21.2) WILD-TYPE        45        14         52         34
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 14(7Q21.2) MUTATED           25       21         3
  AMP PEAK 14(7Q21.2) WILD-TYPE         21       28         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  STAGE I                              6                             4
  STAGE IA                             9                            12
  STAGE IB                            23                            24
  STAGE II                            16                            17
  STAGE IIA                           47                            40
  STAGE IIB                           42                            45
  STAGE III                           14                            14
  STAGE IIIA                          43                            52
  STAGE IIIB                          38                            34
  STAGE IIIC                          25                            21
  STAGE IV                            21                            28
  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      31  66 151  50
  AMP PEAK 14(7Q21.2) WILD-TYPE    24  70 132  74
D14V4, multiclass
       clus
vv      AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  T0+T1                          31                            24
  T2                             66                            70
  T3                            151                           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
  AMP PEAK 14(7Q21.2) MUTATED   107  86  53  49
  AMP PEAK 14(7Q21.2) WILD-TYPE 100 101  45  47
D14V5, multiclass
    clus
vv   AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  N0                         107                           100
  N1                          86                           101
  N2                          53                            45
  N3                          49                            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED   260  18
  AMP PEAK 14(7Q21.2) WILD-TYPE 264  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED    260   18
  AMP PEAK 14(7Q21.2) WILD-TYPE  264   21
   clus
vv  AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  0                         260                           264
  1                          18                            21
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED    76 241
  AMP PEAK 14(7Q21.2) WILD-TYPE 109 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED     76  241
  AMP PEAK 14(7Q21.2) WILD-TYPE  109  199
        clus
vv       AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  FEMALE                          76                           109
  MALE                           241                           199
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED   218  65
  AMP PEAK 14(7Q21.2) WILD-TYPE 227  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED    218   65
  AMP PEAK 14(7Q21.2) WILD-TYPE  227   54
     clus
vv    AMP PEAK 14(7Q21.2) MUTATED AMP PEAK 14(7Q21.2) WILD-TYPE
  NO                          218                           227
  YES                          65                            54
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(7Q21.2) MUTATED      69                        13
  AMP PEAK 14(7Q21.2) WILD-TYPE    65                         4
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 14(7Q21.2) MUTATED                                           1   195
  AMP PEAK 14(7Q21.2) WILD-TYPE                                         0   197
D14V11, multiclass
                                           clus
vv                                          AMP PEAK 14(7Q21.2) MUTATED
  ASIAN                                                              69
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             195
                                           clus
vv                                          AMP PEAK 14(7Q21.2) WILD-TYPE
  ASIAN                                                                65
  BLACK OR AFRICAN AMERICAN                                             4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D14V12, binary
                               cls
clus                              0   1
  AMP PEAK 14(7Q21.2) MUTATED     6 193
  AMP PEAK 14(7Q21.2) WILD-TYPE   5 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7Q21.2) MUTATED      6  193
  AMP PEAK 14(7Q21.2) WILD-TYPE    5  211
                        clus
vv                       AMP PEAK 14(7Q21.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         193
                        clus
vv                       AMP PEAK 14(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           211
[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   126  90
  AMP PEAK 15(8P23.1) WILD-TYPE 228 155
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                          216                           383 
  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                           90                           155 
$`AMP PEAK 15(8P23.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88Y TCGA-CG-4460 TCGA-KB-A93G TCGA-MX-A663 
       18.28        19.99         0.36        21.99        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GO 
       27.35        26.93        25.78        14.30         8.94        16.24 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A8O2 TCGA-JY-A6F8 
       32.45        33.27        35.21        20.78         4.67       122.10 
TCGA-JY-A6FD TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C 
       68.02        21.70        31.56        25.22        24.03         3.16 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR 
       30.25         0.30        21.01        47.93        18.35         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        4.90         7.13        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 
       12.59        12.62        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        16.44        15.35        27.09        22.82 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK 
       18.21        25.08        19.73        26.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 
        6.61         6.97         4.64        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        9.67        34.68        15.95        13.87        13.68        19.33 
TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 
       25.61        19.89        30.90        31.20        44.94        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8284 
       35.84        18.15         9.07        11.44        29.59         8.05 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
        2.66         7.40         4.31        14.04         3.32        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8590 
        7.36        25.05         5.39        25.18        20.22         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J2 
       28.14         7.53        34.98         1.48        27.55        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5799 
       28.34        32.52         0.46        20.42        16.14        13.02 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C 
       11.21        12.76        12.39        12.43        12.30        11.61 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 
        6.58        12.62        15.95        14.01        12.03         0.00 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 
       18.97         7.07        12.00         0.99        28.96        65.10 
TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 
       21.07        12.66        20.91        17.85        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       12.36        11.31        12.33        18.21        14.66        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        36.43        14.76        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 
       22.29         8.38         4.34        21.27        19.53        17.06 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       24.39        22.32        24.30        24.26        22.68        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        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H 
       15.68        13.35        12.59        10.62        63.62        37.64 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8N1 
       19.73        45.67        74.53         6.08        16.67       115.69 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8P2 
       35.61        16.87        19.04        48.79         5.46        38.14 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       30.97        34.29        16.31        22.19         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91K 
       23.41        29.59        64.57        14.33        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 TCGA-VQ-A928 
       18.74        20.81        42.64        60.85         4.54         5.72 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.04        42.54        16.14        27.55        17.26         0.79 

$`AMP PEAK 15(8P23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        22.82        35.97        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-2H-A9GH 
       47.05        22.98        79.07        16.24         0.23        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       58.55         7.63         5.92        13.94         4.21         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT 
        0.85         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-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86        14.50        12.16        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO 
       47.38        23.18         6.28        26.33        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S 
        7.17         1.38        58.59        29.00         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       13.48        16.47        13.22        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 
       12.33        13.38        13.15        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        12.85        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-A8HZ TCGA-LN-A8I0 
       10.52        12.00        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30         2.89         2.30        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42         9.27         8.98        25.81        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        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 
       46.19        18.05        11.24         9.17        15.91        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       14.37         3.42         2.10         1.32         2.66        58.03 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
       11.70        19.56         9.44         7.43        18.35         4.08 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 
        6.18         9.57         6.61        17.29        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
        9.17        32.78        18.05        12.16         8.98        40.21 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       21.90         9.21        36.16        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.69         9.60        32.25         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8373 
       22.19        17.52         0.95        26.33        11.80        14.79 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 
        3.72         9.21         1.12        12.79        27.12         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 
       28.57        12.89         8.98         0.72         0.53         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65         1.15        21.44         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18        13.35        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.07        12.82         6.31        11.31        12.43        12.20 
TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       11.77        20.02         3.02        27.02         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 
        8.05        54.08         4.01        29.98        19.07         9.01 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
      105.07        12.03        15.02         4.01        69.04         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       25.71        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8572 
       13.35        17.19        15.22        15.98        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YY 
       19.50        17.19        21.14        14.27        16.44        13.78 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       26.43        20.32        15.65        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.99        14.47        72.23        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7133 
       22.29        59.54         5.03        13.58         0.56        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        18.15        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT 
        0.76         5.59        22.75        11.77        21.37         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        6.58        20.25        21.17        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74         6.51        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        36.95         3.72        14.04        18.21         8.52 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PF 
       21.73        37.41        37.22         7.73        46.26         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PZ 
       12.79        17.85         1.87        15.65        13.35        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       39.45        11.70        32.88         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
       55.56         9.04         2.01        55.43         6.58        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       32.94        17.13        54.12        26.04        12.43 

  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE 
                         0.00                          0.13 
  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 
                       16.375                        13.220 
[1] "0.0 - 122.1 (16.4)" "0.1 - 122.3 (13.2)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(8P23.1) MUTATED         3       10       21       13        24
  AMP PEAK 15(8P23.1) WILD-TYPE       7       11       26       20        63
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(8P23.1) MUTATED          37         8         34         21
  AMP PEAK 15(8P23.1) WILD-TYPE        50        20         61         51
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 15(8P23.1) MUTATED           19       20         2
  AMP PEAK 15(8P23.1) WILD-TYPE         27       29         2
D15V3, multiclass
            clus
vv           AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                            10                            11
  STAGE IB                            21                            26
  STAGE II                            13                            20
  STAGE IIA                           24                            63
  STAGE IIB                           37                            50
  STAGE III                            8                            20
  STAGE IIIA                          34                            61
  STAGE IIIB                          21                            51
  STAGE IIIC                          19                            27
  STAGE IV                            20                            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
  AMP PEAK 15(8P23.1) MUTATED      24  50  95  50
  AMP PEAK 15(8P23.1) WILD-TYPE    31  86 188  74
D15V4, multiclass
       clus
vv      AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  T0+T1                          24                            31
  T2                             50                            86
  T3                             95                           188
  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  69  33  39
  AMP PEAK 15(8P23.1) WILD-TYPE 134 118  65  57
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  N0                          73                           134
  N1                          69                           118
  N2                          33                            65
  N3                          39                            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"
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED   194  14
  AMP PEAK 15(8P23.1) WILD-TYPE 330  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED    194   14
  AMP PEAK 15(8P23.1) WILD-TYPE  330   25
   clus
vv  AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  0                         194                           330
  1                          14                            25
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED    87 142
  AMP PEAK 15(8P23.1) WILD-TYPE  98 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED     87  142
  AMP PEAK 15(8P23.1) WILD-TYPE   98  298
        clus
vv       AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  FEMALE                          87                            98
  MALE                           142                           298
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED   167  39
  AMP PEAK 15(8P23.1) WILD-TYPE 278  80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED    167   39
  AMP PEAK 15(8P23.1) WILD-TYPE  278   80
     clus
vv    AMP PEAK 15(8P23.1) MUTATED AMP PEAK 15(8P23.1) WILD-TYPE
  NO                          167                           278
  YES                          39                            80
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(8P23.1) MUTATED      41                         6
  AMP PEAK 15(8P23.1) WILD-TYPE    93                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 15(8P23.1) MUTATED                                           0   148
  AMP PEAK 15(8P23.1) WILD-TYPE                                         1   244
D15V11, multiclass
                                           clus
vv                                          AMP PEAK 15(8P23.1) MUTATED
  ASIAN                                                              41
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             148
                                           clus
vv                                          AMP PEAK 15(8P23.1) WILD-TYPE
  ASIAN                                                                93
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                               cls
clus                              0   1
  AMP PEAK 15(8P23.1) MUTATED     5 143
  AMP PEAK 15(8P23.1) WILD-TYPE   6 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(8P23.1) MUTATED      5  143
  AMP PEAK 15(8P23.1) WILD-TYPE    6  261
                        clus
vv                       AMP PEAK 15(8P23.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       AMP PEAK 15(8P23.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           261
[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   155 103
  AMP PEAK 16(8P11.21) WILD-TYPE 199 142
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           258                            341 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           103                            142 
$`AMP PEAK 16(8P11.21) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        18.28        19.99         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        21.99        20.15        26.93        14.30        58.55 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL 
       13.94         8.94        16.24         4.21        33.27        35.21 
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A8O2 
       20.78        18.64         3.88        17.03        12.82         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93D 
      122.10        44.75        68.02         3.68        23.18        31.56 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OM 
       24.03         3.16        30.25         0.30        26.33        47.93 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
       18.35         3.32         3.16         4.90         7.13         7.43 
TCGA-L5-A891 TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.75        13.55        13.22         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49P 
        8.71        13.41        10.36         5.92        10.45        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 
       13.15        15.35        12.59        12.62        12.46        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.59        12.85        11.54        12.33        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ 
       12.33        13.18         0.13        12.85        12.26         7.59 
TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        5.06        53.95        15.78        12.69         7.00        20.38 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EW TCGA-VR-A8EX 
       15.35         8.98        27.09        22.82         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-B7-5816 TCGA-B7-A5TJ 
       18.18        46.19        15.91         2.10        26.70        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 
        9.47         9.44         6.61         6.97         4.64        30.90 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        4.08         9.34         9.67        34.68        15.95        13.87 
TCGA-BR-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        44.94         9.21        35.24        35.84        39.78 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 
        3.45         9.07        29.56        29.59         8.05        29.42 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
        7.40        31.10         4.31         3.32        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.05         5.39        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       28.14         7.53         8.22         7.53        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       27.55        28.34        32.52         0.46        20.42        21.44 
TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8530 TCGA-CD-8536 
       16.14        13.02        11.21        12.59        12.39        12.43 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
       12.30        11.61         6.58        12.62        20.02        15.95 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4469 TCGA-CG-4472 
        7.99        14.01        12.03         0.00         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.97         0.99        12.03        15.02        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 
       69.04        21.07        20.91        17.85        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX 
       12.36        12.33        14.66        20.91         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 
       14.76        11.24        11.31        11.44        22.29         8.38 
TCGA-D7-A748 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        4.34        21.27        19.53         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21        30.51        26.47        24.39        28.96        22.32 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN 
       24.30        24.26        22.68        24.20         3.25        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         0.10         0.26         2.10        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
       23.80        14.07        15.68        18.38        13.35         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59         6.51        10.62        15.75         5.56        63.62 
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        74.53 
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        38.14        30.97        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        29.59        64.57        21.83        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 TCGA-VQ-A928 
       32.88         1.71        42.64        60.85         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       66.81        21.04        43.66        38.93        17.26         0.79 

$`AMP PEAK 16(8P11.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A88T TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       22.82         5.16        47.05        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK 
        0.23         9.86        27.35        25.78        31.27         7.63 
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC 
        5.92        32.45         7.69         0.85         2.63        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30         0.53         0.79        23.41         9.96        14.86 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E 
       14.50        12.16        41.52        47.38        21.70        25.22 
TCGA-KH-A6WC TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
        6.28        32.61        21.01         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       29.00        15.48         2.60        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU 
       55.50         2.66        12.92        13.48        16.47        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09        10.85        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 
       13.38        13.25        12.59        12.49        22.39        15.52 
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-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.23        13.38        12.03        33.11         7.82         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
       16.31         7.04        38.40         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO 
        2.30         5.29         3.42        16.44         9.27        25.81 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G 
       12.43         1.55        18.31        33.70        52.27        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 
        3.42         1.32         2.66        19.73        58.03        11.70 
TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-4279 
       19.56         7.43        18.35         4.08         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
        6.61        19.33        39.12        26.10        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7715 
       18.05         8.98        40.21        21.90        36.16        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       18.15        15.32        28.73        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 
       11.44         0.69         9.60        32.25         0.56         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
       19.96         2.20        15.58         6.18        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52         0.95        26.33        14.04        11.80 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8592 
       14.79         3.72        25.18         9.21         1.12         6.28 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY 
       10.68        34.13        13.87         6.08        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98         0.72        14.17         0.53         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       20.65         1.15         5.13        13.41        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.35        12.10        12.76        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 
        6.31        11.31        12.43        12.20        11.77         3.02 
TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       27.02         1.02         8.05        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       19.07         9.01        18.97        30.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 
        0.99         6.02       105.07         4.01         7.99        25.71 
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-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8570 
       13.35        17.19        15.22        15.98        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT 
       16.80        19.50        17.19        18.21        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        26.43        20.32        15.65        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        72.23        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-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       13.58         0.56        63.06         1.51         5.92        18.15 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GF 
       22.82        21.07         0.76         5.59        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 
       11.77        21.37         6.51         6.58        20.25        12.95 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       21.17        33.40        36.36         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.46        19.53         6.44        11.70        13.51         2.53 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       36.95        14.04        18.21         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-A8N2 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU 
      116.38        57.44         8.94        35.61         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       37.22         7.73        46.26        22.19         2.50        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       17.85         1.87        15.65        13.35        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y 
       39.45        11.70        61.22        20.81         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
       55.56         9.04         2.01        55.43         6.58         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        26.04        16.14        27.55        12.43 

  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                          0.00                           0.23 
  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 
                         14.04                          13.78 
[1] "0.0 - 122.1 (14.0)" "0.2 - 122.3 (13.8)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(8P11.21) MUTATED         5       12       22       15        31
  AMP PEAK 16(8P11.21) WILD-TYPE       5        9       25       18        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(8P11.21) MUTATED          46        16         37         23
  AMP PEAK 16(8P11.21) WILD-TYPE        41        12         58         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 16(8P11.21) MUTATED           24       19         3
  AMP PEAK 16(8P11.21) WILD-TYPE         22       30         1
D16V3, multiclass
            clus
vv           AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                             12                              9
  STAGE IB                             22                             25
  STAGE II                             15                             18
  STAGE IIA                            31                             56
  STAGE IIB                            46                             41
  STAGE III                            16                             12
  STAGE IIIA                           37                             58
  STAGE IIIB                           23                             49
  STAGE IIIC                           24                             22
  STAGE IV                             19                             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
  AMP PEAK 16(8P11.21) MUTATED      29  59 116  55
  AMP PEAK 16(8P11.21) WILD-TYPE    26  77 167  69
D16V4, multiclass
       clus
vv      AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  T0+T1                           29                             26
  T2                              59                             77
  T3                             116                            167
  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    91  90  34  39
  AMP PEAK 16(8P11.21) WILD-TYPE 116  97  64  57
D16V5, multiclass
    clus
vv   AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  N0                           91                            116
  N1                           90                             97
  N2                           34                             64
  N3                           39                             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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED   234  15
  AMP PEAK 16(8P11.21) WILD-TYPE 290  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED    234   15
  AMP PEAK 16(8P11.21) WILD-TYPE  290   24
   clus
vv  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  0                          234                            290
  1                           15                             24
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    91 181
  AMP PEAK 16(8P11.21) WILD-TYPE  94 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     91  181
  AMP PEAK 16(8P11.21) WILD-TYPE   94  259
        clus
vv       AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           91                             94
  MALE                            181                            259
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED   195  50
  AMP PEAK 16(8P11.21) WILD-TYPE 250  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED    195   50
  AMP PEAK 16(8P11.21) WILD-TYPE  250   69
     clus
vv    AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  NO                           195                            250
  YES                           50                             69
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(8P11.21) MUTATED      61                         6
  AMP PEAK 16(8P11.21) WILD-TYPE    73                        11
                                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     166
  AMP PEAK 16(8P11.21) WILD-TYPE   226
D16V11, multiclass
                                           clus
vv                                          AMP PEAK 16(8P11.21) MUTATED
  ASIAN                                                               61
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              166
                                           clus
vv                                          AMP PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                                 73
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED     4 173
  AMP PEAK 16(8P11.21) WILD-TYPE   7 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED      4  173
  AMP PEAK 16(8P11.21) WILD-TYPE    7  231
                        clus
vv                       AMP PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          173
                        clus
vv                       AMP PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            231
[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   257 178
  AMP PEAK 17(8Q24.21) WILD-TYPE  97  67
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           435                            164 
  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                           178                             67 
$`AMP PEAK 17(8Q24.21) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI 
       60.39        34.85        18.28         4.31        24.00        19.99 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
        0.36        35.97        27.12        20.02        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       27.35        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         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        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12         3.88         0.53        17.03         0.79 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       12.82         9.96         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       31.56        24.03         3.16        30.25         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       21.01        47.93        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A891 
       58.59         4.90         7.13         7.43         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50        12.92        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       21.37         8.71        13.41        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
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-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.85        11.54        12.33        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       13.38        13.18         0.13        12.85        12.26         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.59         5.06        16.31         7.04        38.40        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89        12.69         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44        15.35         9.27         8.98        27.09        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        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        46.19        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 
       41.23         3.42         2.10         1.32        19.73        58.03 
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        9.57        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6802 
        9.17        25.61        19.89        12.16        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        44.94         9.21        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       33.21        14.43         0.69        29.59         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         2.20        15.58         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 
       13.08        26.33         4.31        14.04         3.32        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 
       12.79         9.34        28.14         7.53        24.79        32.58 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        13.87         7.53        34.98         1.48 
TCGA-BR-A4IU TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4PE 
       27.55         0.72        14.17        28.34         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       21.44        16.14        13.15        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 
       12.59        12.53         7.17        12.33        12.39        15.39 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 
        6.58        12.62        20.02         3.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00        18.97         7.07        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
       36.00         0.99        12.03        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
       18.84        17.85        13.35        17.19        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8576 
       12.79        12.36        11.31        12.33        24.72        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        36.43        14.76 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 
        4.34        19.96         0.62         7.99        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
        3.48        19.53        17.06         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       18.15        28.96        22.32         0.76        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        29.00        23.84        23.80        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       33.40         3.45         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        15.75         2.53         5.56        63.62        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       74.53         6.08         4.60         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
       16.67       115.69        71.38         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-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       13.02        18.48        43.36        37.41        38.14         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PX 
       17.85         1.87         9.27        23.41        29.59        64.57 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       39.45        21.83        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A927 
       60.85         9.50        55.56         9.04         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81        21.04        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        32.94        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

$`AMP PEAK 17(8Q24.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T TCGA-Q9-A6FU TCGA-IG-A4P3 
       15.68         8.94         4.70        22.82         5.16        18.64 
TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-JY-A6FH TCGA-JY-A93E TCGA-KH-A6WC 
        9.30        23.41        14.86        47.38        25.22         6.28 
TCGA-L5-A4OF TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       26.33         7.17        29.00        15.48        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NU TCGA-L5-A8NV 
        3.02         2.66        13.48        16.47        83.24        52.57 
TCGA-LN-A4A8 TCGA-LN-A5U5 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6XQ 
       15.52         4.47        12.03        33.11         7.82         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-AA4G 
        9.30         2.30         3.42        25.81         1.55        18.05 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4183 
       18.21        14.37         2.66        11.70        19.56         6.61 
TCGA-BR-4188 TCGA-BR-4253 TCGA-BR-4280 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
        7.43         4.08         6.61        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7722 
       32.78        18.05         8.98        21.90        36.16        15.32 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8361 
       37.25        11.44        32.25         0.56        19.96        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 TCGA-BR-8373 
        0.26        22.19        17.52         0.95        11.80        14.79 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 
       25.18         1.12        27.12         6.28        26.73        31.96 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY 
        9.86        20.88        34.13         6.08        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
        8.98         0.53         0.66        32.52        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8524 
        1.15         5.13        13.41        13.02        13.18        12.76 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MH 
       12.30        12.59        11.64        12.07        11.31        12.20 
TCGA-CD-A4MI TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5719 
       11.77        27.02         1.02         9.01        30.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-6519 
        0.99         6.02       105.07        15.02        25.71        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.54        18.61        10.26        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A74B 
       18.21        21.14        13.78        26.43        20.32         7.13 
TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       14.47        11.38        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 
       13.58        63.06         1.51        22.82        21.07         5.59 
TCGA-HU-A4GJ TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 
       21.37        20.25        12.95        21.17        36.36        18.81 
TCGA-IN-AB1X TCGA-KB-A93J TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       13.51        36.95         5.13       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N5 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PF 
      116.38        57.44        21.73        37.22        46.26         2.50 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
       15.65        13.35        14.33        73.41        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A94P TCGA-VQ-AA69 
       20.81         9.73         2.01        55.43         2.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6G 
       38.93        26.04 

  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE 
                          0.00                           0.26 
  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 
                         13.38                          15.40 
[1] "0.0 - 122.1 (13.4)" "0.3 - 122.3 (15.4)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(8Q24.21) MUTATED         8       17       33       23        60
  AMP PEAK 17(8Q24.21) WILD-TYPE       2        4       14       10        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(8Q24.21) MUTATED          66        25         69         48
  AMP PEAK 17(8Q24.21) WILD-TYPE        21         3         26         24
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 17(8Q24.21) MUTATED           33       35         3
  AMP PEAK 17(8Q24.21) WILD-TYPE         13       14         1
D17V3, multiclass
            clus
vv           AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  STAGE I                               8                              2
  STAGE IA                             17                              4
  STAGE IB                             33                             14
  STAGE II                             23                             10
  STAGE IIA                            60                             27
  STAGE IIB                            66                             21
  STAGE III                            25                              3
  STAGE IIIA                           69                             26
  STAGE IIIB                           48                             24
  STAGE IIIC                           33                             13
  STAGE IV                             35                             14
  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      44 100 206  82
  AMP PEAK 17(8Q24.21) WILD-TYPE    11  36  77  42
D17V4, multiclass
       clus
vv      AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  T0+T1                           44                             11
  T2                             100                             36
  T3                             206                             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   147 142  64  72
  AMP PEAK 17(8Q24.21) WILD-TYPE  60  45  34  24
D17V5, multiclass
    clus
vv   AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  N0                          147                             60
  N1                          142                             45
  N2                           64                             34
  N3                           72                             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   380  27
  AMP PEAK 17(8Q24.21) WILD-TYPE 144  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED    380   27
  AMP PEAK 17(8Q24.21) WILD-TYPE  144   12
   clus
vv  AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  0                          380                            144
  1                           27                             12
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED   126 328
  AMP PEAK 17(8Q24.21) WILD-TYPE  59 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED    126  328
  AMP PEAK 17(8Q24.21) WILD-TYPE   59  112
        clus
vv       AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  FEMALE                          126                             59
  MALE                            328                            112
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED   321  86
  AMP PEAK 17(8Q24.21) WILD-TYPE 124  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED    321   86
  AMP PEAK 17(8Q24.21) WILD-TYPE  124   33
     clus
vv    AMP PEAK 17(8Q24.21) MUTATED AMP PEAK 17(8Q24.21) WILD-TYPE
  NO                           321                            124
  YES                           86                             33
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(8Q24.21) MUTATED     100                        15
  AMP PEAK 17(8Q24.21) WILD-TYPE    34                         2
                                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     275
  AMP PEAK 17(8Q24.21) WILD-TYPE   117
D17V11, multiclass
                                           clus
vv                                          AMP PEAK 17(8Q24.21) MUTATED
  ASIAN                                                              100
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              275
                                           clus
vv                                          AMP PEAK 17(8Q24.21) WILD-TYPE
  ASIAN                                                                 34
  BLACK OR AFRICAN AMERICAN                                              2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                117
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK 17(8Q24.21) MUTATED     8 289
  AMP PEAK 17(8Q24.21) WILD-TYPE   3 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(8Q24.21) MUTATED      8  289
  AMP PEAK 17(8Q24.21) WILD-TYPE    3  115
                        clus
vv                       AMP PEAK 17(8Q24.21) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          289
                        clus
vv                       AMP PEAK 17(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            115
[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    55  30
  AMP PEAK 18(9P24.1) WILD-TYPE 299 215
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           85                           514 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           30                           215 
$`AMP PEAK 18(9P24.1) MUTATED`
TCGA-L5-A43J TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX 
        4.31         0.36        27.12        21.99        16.24         0.23 
TCGA-KB-A93G TCGA-2H-A9GL TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-JY-A6F8 
       20.15         5.92        17.03        12.82         9.96       122.10 
TCGA-JY-A939 TCGA-L5-A4OU TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L7-A6VZ TCGA-LN-A49K 
       21.70        29.00        12.92         5.49        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.43        13.41        13.15        12.59        13.18        13.38 
TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-Z6-AAPN 
       12.85         7.82        16.31        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        35.84 
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 
       24.79        12.89         0.53        21.44        13.41        13.18 
TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4477 
       12.82        12.43        12.20         7.99         8.05        30.97 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EY TCGA-EQ-5647 
       15.22        12.36        12.33        14.27        11.44         0.62 
TCGA-F1-6875 TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 
       72.23        21.27        77.29        52.21        30.51        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP 
       22.82        21.07         0.76        24.26        22.75         8.98 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-KB-A6F7 TCGA-R5-A7ZI 
        2.10        12.95        23.80         3.39        63.62        74.53 
TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A94T 
        5.46        46.26        23.41        32.88        42.64        11.24 
TCGA-VQ-AA6D 
       17.13 

$`AMP PEAK 18(9P24.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82        35.97         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       47.05        22.98        79.07         9.86        27.35        26.93 
TCGA-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-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A7DP 
        3.88         9.30         0.53         0.79        23.41        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
        6.28         3.16        30.25         0.30        26.33        32.61 
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-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        3.16        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        13.48        16.47        13.55        13.22         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       10.85        10.45        12.66        12.33        13.38        15.35 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        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        12.85        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-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.03        12.33        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       12.26        33.11         8.02         7.59         5.06         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         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 
       16.44        15.35         9.27         8.98        25.81        27.09 
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-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       33.70        52.27        46.19        18.05        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32        19.73        58.03        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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       25.61         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       33.21        37.25        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        8.05        29.42        19.96        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.02        13.15        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-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-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        12.00         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.98        12.79        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A72C 
        4.34        19.96         7.13         7.99        14.47        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-A9TM TCGA-HF-7133 
        5.03        13.58         0.56         5.52         6.21        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        24.39        18.15        22.32 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        22.68        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         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
       20.25         0.26        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21         8.52         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-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-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81        21.04         2.66        42.54        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                         0.23                          0.00 
  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 
                        13.15                         14.12 
[1] "0.2 - 122.1 (13.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(9P24.1) MUTATED         1        4       10        3        15
  AMP PEAK 18(9P24.1) WILD-TYPE       9       17       37       30        72
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(9P24.1) MUTATED          11         3         12         12
  AMP PEAK 18(9P24.1) WILD-TYPE        76        25         83         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(9P24.1) MUTATED            9        6         0
  AMP PEAK 18(9P24.1) WILD-TYPE         37       43         4
D18V3, multiclass
            clus
vv           AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             4                            17
  STAGE IB                            10                            37
  STAGE II                             3                            30
  STAGE IIA                           15                            72
  STAGE IIB                           11                            76
  STAGE III                            3                            25
  STAGE IIIA                          12                            83
  STAGE IIIB                          12                            60
  STAGE IIIC                           9                            37
  STAGE IV                             6                            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
  AMP PEAK 18(9P24.1) MUTATED      10  20  38  21
  AMP PEAK 18(9P24.1) WILD-TYPE    45 116 245 103
D18V4, multiclass
       clus
vv      AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  T0+T1                          10                            45
  T2                             20                           116
  T3                             38                           245
  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    36  24  10  17
  AMP PEAK 18(9P24.1) WILD-TYPE 171 163  88  79
D18V5, multiclass
    clus
vv   AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  N0                          36                           171
  N1                          24                           163
  N2                          10                            88
  N3                          17                            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"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    78   5
  AMP PEAK 18(9P24.1) WILD-TYPE 446  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     78    5
  AMP PEAK 18(9P24.1) WILD-TYPE  446   34
   clus
vv  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  0                          78                           446
  1                           5                            34
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    23  68
  AMP PEAK 18(9P24.1) WILD-TYPE 162 372
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     23   68
  AMP PEAK 18(9P24.1) WILD-TYPE  162  372
        clus
vv       AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  FEMALE                          23                           162
  MALE                            68                           372
[1] 2 2
[1] FALSE
D18V8, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    61  21
  AMP PEAK 18(9P24.1) WILD-TYPE 384  98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     61   21
  AMP PEAK 18(9P24.1) WILD-TYPE  384   98
     clus
vv    AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  NO                           61                           384
  YES                          21                            98
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(9P24.1) MUTATED      26                         2
  AMP PEAK 18(9P24.1) WILD-TYPE   108                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(9P24.1) MUTATED                                           0    48
  AMP PEAK 18(9P24.1) WILD-TYPE                                         1   344
D18V11, multiclass
                                           clus
vv                                          AMP PEAK 18(9P24.1) MUTATED
  ASIAN                                                              26
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              48
                                           clus
vv                                          AMP PEAK 18(9P24.1) WILD-TYPE
  ASIAN                                                               108
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               344
[1] 4 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, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED     2  61
  AMP PEAK 18(9P24.1) WILD-TYPE   9 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED      2   61
  AMP PEAK 18(9P24.1) WILD-TYPE    9  343
                        clus
vv                       AMP PEAK 18(9P24.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       AMP PEAK 18(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           343
[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    75  53
  AMP PEAK 19(9P13.3) WILD-TYPE 279 192
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                          128                           471 
  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                           53                           192 
$`AMP PEAK 19(9P13.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 
       18.28         4.31         0.36        35.97        27.12        47.05 
TCGA-CG-4460 TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL 
       21.99         0.23        20.15        25.78        14.30         5.92 
TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4ON 
       12.82       122.10        68.02         0.30        32.61        18.35 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A8NE TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K 
        3.16        29.00        55.50        46.09        10.36         5.92 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A4MQ TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       13.41        12.33        12.33        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A8W5 
       13.38        12.85         7.82         5.06        16.31        15.78 
TCGA-S8-A6BW TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7D 
       20.38         9.27        22.82        18.18        52.27         9.17 
TCGA-XP-A8T6 TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-6707 
       25.08         1.32        58.03         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        35.84        18.15        33.21         9.60         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-A44U 
       19.96         2.20        20.22        12.79        24.79        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5798 
        7.53        34.98         0.53        20.42        21.44        13.41 
TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8535 TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4437 
       13.18        12.53        12.82        12.20         7.99         8.05 
TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.97        30.97        20.91        17.19        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EX 
       12.36        12.33        18.21        14.27        14.76        11.31 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7829 
       11.44        22.29         8.38         0.62        21.27        19.53 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 
       77.29        52.21        30.51        28.96         0.76        24.26 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 
       22.75         8.98        12.95        23.80        21.17         3.39 
TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A8MV 
       15.75        63.62         8.52        74.53         6.08       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PE 
      115.69        35.61        48.79         5.46        46.26        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q 
        2.70        17.85        23.41        13.35        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A928 TCGA-VQ-A92D 
       32.88         1.71         9.50        55.56         5.72        66.81 
TCGA-VQ-A94T TCGA-VQ-AA6F 
       11.24        54.12 

$`AMP PEAK 19(9P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 
       19.99        22.82         5.16        20.02        22.98        79.07 
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GJ 
       16.24         9.86        27.35        26.93        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         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-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-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75         3.68        41.52        47.38        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-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25        26.33        21.01        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
       12.92        13.48        16.47        13.55        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-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S 
       10.85        10.45        12.66        12.43        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        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        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       11.54        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.00        12.23        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         8.02         7.59         7.04        38.40         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         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO 
        5.29         3.42        16.44        15.35         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        46.19        18.05        11.24        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         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-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       26.10         9.17        32.78        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
        3.72         5.39        25.18         9.21         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
        0.46        20.65         1.15        16.14         5.13        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       15.39        12.07        12.43         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        11.77        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02        15.95         1.02        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       14.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       17.85        13.35        15.98        12.79        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        13.78        26.43        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       20.32        15.65         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        11.38         3.48        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        6.21        63.06        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        22.82        21.07        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        29.00        23.84        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J 
       11.70        13.51         2.53         5.56        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A804 
        3.72        19.73        14.04        45.67        18.21         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       19.04         5.79         0.92        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       30.97        34.29        16.31         2.50        12.79         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
        9.27        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A91W 
       39.45        11.70        21.83        61.22        42.64        60.85 
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-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        17.13        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE 
                         0.23                          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 
                       15.765                        13.550 
[1] "0.2 - 122.3 (15.8)" "0.0 - 116.4 (13.6)"
[1] "hr=" "1.1"
D19V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(9P13.3) MUTATED         2        6       17        5        13
  AMP PEAK 19(9P13.3) WILD-TYPE       8       15       30       28        74
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(9P13.3) MUTATED          14         9         25         17
  AMP PEAK 19(9P13.3) WILD-TYPE        73        19         70         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(9P13.3) MUTATED            6       11         1
  AMP PEAK 19(9P13.3) WILD-TYPE         40       38         3
D19V3, multiclass
            clus
vv           AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             6                            15
  STAGE IB                            17                            30
  STAGE II                             5                            28
  STAGE IIA                           13                            74
  STAGE IIB                           14                            73
  STAGE III                            9                            19
  STAGE IIIA                          25                            70
  STAGE IIIB                          17                            55
  STAGE IIIC                           6                            40
  STAGE IV                            11                            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
  AMP PEAK 19(9P13.3) MUTATED      12  31  65  20
  AMP PEAK 19(9P13.3) WILD-TYPE    43 105 218 104
D19V4, multiclass
       clus
vv      AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  T0+T1                          12                            43
  T2                             31                           105
  T3                             65                           218
  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    41  45  19  21
  AMP PEAK 19(9P13.3) WILD-TYPE 166 142  79  75
D19V5, multiclass
    clus
vv   AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  N0                          41                           166
  N1                          45                           142
  N2                          19                            79
  N3                          21                            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"
D19V6, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED   111   7
  AMP PEAK 19(9P13.3) WILD-TYPE 413  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED    111    7
  AMP PEAK 19(9P13.3) WILD-TYPE  413   32
   clus
vv  AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  0                         111                           413
  1                           7                            32
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED    36  96
  AMP PEAK 19(9P13.3) WILD-TYPE 149 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED     36   96
  AMP PEAK 19(9P13.3) WILD-TYPE  149  344
        clus
vv       AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  FEMALE                          36                           149
  MALE                            96                           344
[1] 2 2
[1] FALSE
D19V8, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED    94  30
  AMP PEAK 19(9P13.3) WILD-TYPE 351  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED     94   30
  AMP PEAK 19(9P13.3) WILD-TYPE  351   89
     clus
vv    AMP PEAK 19(9P13.3) MUTATED AMP PEAK 19(9P13.3) WILD-TYPE
  NO                           94                           351
  YES                          30                            89
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(9P13.3) MUTATED      28                         4
  AMP PEAK 19(9P13.3) WILD-TYPE   106                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(9P13.3) MUTATED                                           0    79
  AMP PEAK 19(9P13.3) WILD-TYPE                                         1   313
D19V11, multiclass
                                           clus
vv                                          AMP PEAK 19(9P13.3) MUTATED
  ASIAN                                                              28
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              79
                                           clus
vv                                          AMP PEAK 19(9P13.3) WILD-TYPE
  ASIAN                                                               106
  BLACK OR AFRICAN AMERICAN                                            13
  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"
D19V12, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P13.3) MUTATED     4  77
  AMP PEAK 19(9P13.3) WILD-TYPE   7 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P13.3) MUTATED      4   77
  AMP PEAK 19(9P13.3) WILD-TYPE    7  327
                        clus
vv                       AMP PEAK 19(9P13.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       AMP PEAK 19(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           327
[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   119  58
  AMP PEAK 20(9Q34.3) WILD-TYPE 235 187
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                          177                           422 
  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                           58                           187 
$`AMP PEAK 20(9Q34.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4475 
       60.39         4.31         0.36        27.12        20.02        22.98 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GL TCGA-IC-A6RE 
       16.24        20.15        27.35        31.27         5.92         7.69 
TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
        0.53        12.82         9.96        14.50       122.10         3.68 
TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OU 
       47.38        23.18         3.16         3.32         1.38        29.00 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NL TCGA-L5-A8NS 
        7.13         2.60         3.75        55.50        13.22        13.41 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       46.09        10.36         5.92        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A9 
       13.38        12.59        12.62        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-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6Y0 
       13.38        12.85        12.26         8.02        16.31        53.95 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-VR-A8ER TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
        2.30        20.38        12.43        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       46.19        18.05         9.17        14.37         1.32         2.66 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6564 
        9.47         9.44         6.61        18.35        17.29        26.10 
TCGA-BR-6707 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       19.89         9.21        35.24        35.84        33.63        18.15 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
       33.21        11.44         9.60         2.66         2.20         6.18 
TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A44U TCGA-BR-A4CQ 
       31.10        20.22        12.79        32.58        13.87        34.98 
TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 
        0.53         0.46        20.65        20.42        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 TCGA-CG-4304 
       12.10        12.82        12.30        12.43         3.02        27.02 
TCGA-CG-4436 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-5578 
        7.99        19.07        18.97        30.97        36.00        12.66 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-A4YT 
       20.91        17.19        15.22        12.36        11.31        14.27 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       36.43        14.76        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A448 
       15.65         8.38         4.34         0.62        72.23        21.27 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GP 
        1.51        28.96         0.76        24.26        25.81         8.98 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        6.58        23.80        33.40         3.45        18.81         3.39 
TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A804 
       12.59         5.56        63.62        45.67        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU 
       11.05       122.30       115.69        35.61        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91N 
       18.48        43.36        37.41        46.26        14.33        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       20.81        32.88         1.71        42.64         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6F 
        9.04         5.72        66.81        11.24        43.66        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`AMP PEAK 20(9Q34.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 
       19.99        22.82        35.97         5.16        47.05        21.99 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       79.07         0.23         9.86        26.93        25.78        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD 
       23.41        14.86         4.67        12.16        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        31.56        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX 
       18.35         7.17         3.16        58.59         4.90         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       15.48        25.12         7.40         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        16.47        13.55         7.76         5.49        21.37 
TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
        8.71        83.24        52.57        10.85        10.45        12.66 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.15        15.35        13.25        12.46        12.59        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HX 
       22.39        12.85        15.52        13.22        25.25        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 
       12.03        12.33        13.18         0.13        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30        15.78         2.89        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82         1.55        18.31         8.12        28.11 
TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.10        19.73        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
       11.01         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-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 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        0.56        29.42        19.96        15.58         7.40        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        31.96         9.86        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.41        13.02        13.35        11.21        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       11.64        15.39        12.07        12.43         6.31        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-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-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       29.98        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-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-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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
       18.54        18.61        17.85        13.35        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.79        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       13.78        26.43        11.24        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        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-A9TM 
       17.06        59.54         5.03        13.58         0.56         6.21 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        24.39        18.15        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       14.07        15.68        36.36        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.44         6.74         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         2.53        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       19.73        14.04        18.21         8.52         6.08         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13        16.67        37.91        40.64       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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        13.25        13.02        21.73        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        13.35        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 
       11.70        21.83        61.22        60.85         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         4.54         6.58        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        17.13        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        17.26 

  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE 
                         0.36                          0.00 
  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 
                       13.410                        14.025 
[1] "0.4 - 122.3 (13.4)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1.5"
D20V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(9Q34.3) MUTATED         2        7       16        7        23
  AMP PEAK 20(9Q34.3) WILD-TYPE       8       14       31       26        64
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(9Q34.3) MUTATED          31         8         32         17
  AMP PEAK 20(9Q34.3) WILD-TYPE        56        20         63         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(9Q34.3) MUTATED           11       15         0
  AMP PEAK 20(9Q34.3) WILD-TYPE         35       34         4
D20V3, multiclass
            clus
vv           AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             7                            14
  STAGE IB                            16                            31
  STAGE II                             7                            26
  STAGE IIA                           23                            64
  STAGE IIB                           31                            56
  STAGE III                            8                            20
  STAGE IIIA                          32                            63
  STAGE IIIB                          17                            55
  STAGE IIIC                          11                            35
  STAGE IV                            15                            34
  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      15  43  89  29
  AMP PEAK 20(9Q34.3) WILD-TYPE    40  93 194  95
D20V4, multiclass
       clus
vv      AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  T0+T1                          15                            40
  T2                             43                            93
  T3                             89                           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    55  63  32  24
  AMP PEAK 20(9Q34.3) WILD-TYPE 152 124  66  72
D20V5, multiclass
    clus
vv   AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  N0                          55                           152
  N1                          63                           124
  N2                          32                            66
  N3                          24                            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"
D20V6, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED   158  10
  AMP PEAK 20(9Q34.3) WILD-TYPE 366  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED    158   10
  AMP PEAK 20(9Q34.3) WILD-TYPE  366   29
   clus
vv  AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  0                         158                           366
  1                          10                            29
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED    44 141
  AMP PEAK 20(9Q34.3) WILD-TYPE 141 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED     44  141
  AMP PEAK 20(9Q34.3) WILD-TYPE  141  299
        clus
vv       AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  FEMALE                          44                           141
  MALE                           141                           299
[1] 2 2
[1] FALSE
D20V8, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED   121  45
  AMP PEAK 20(9Q34.3) WILD-TYPE 324  74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED    121   45
  AMP PEAK 20(9Q34.3) WILD-TYPE  324   74
     clus
vv    AMP PEAK 20(9Q34.3) MUTATED AMP PEAK 20(9Q34.3) WILD-TYPE
  NO                          121                           324
  YES                          45                            74
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(9Q34.3) MUTATED      44                         6
  AMP PEAK 20(9Q34.3) WILD-TYPE    90                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 20(9Q34.3) MUTATED                                           0   109
  AMP PEAK 20(9Q34.3) WILD-TYPE                                         1   283
D20V11, multiclass
                                           clus
vv                                          AMP PEAK 20(9Q34.3) MUTATED
  ASIAN                                                              44
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             109
                                           clus
vv                                          AMP PEAK 20(9Q34.3) WILD-TYPE
  ASIAN                                                                90
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               283
[1] 4 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, binary
                               cls
clus                              0   1
  AMP PEAK 20(9Q34.3) MUTATED     4 114
  AMP PEAK 20(9Q34.3) WILD-TYPE   7 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 20(9Q34.3) MUTATED      4  114
  AMP PEAK 20(9Q34.3) WILD-TYPE    7  290
                        clus
vv                       AMP PEAK 20(9Q34.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       AMP PEAK 20(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           290
[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    99  64
  AMP PEAK 21(10P11.22) WILD-TYPE 255 181
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                            163                             436 
  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                             64                             181 
$`AMP PEAK 21(10P11.22) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-MX-A663 
       15.68        18.28        47.05        21.99         0.23         9.86 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       26.93        25.78        58.55        16.24        32.45         7.69 
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        26.33 
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        13.38 
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        12.85 
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        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-Z6-A8JE 
        1.55        18.31        52.27        46.19        18.21         2.10 
TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6457 
        1.32        58.03         6.61         4.08        17.29        13.68 
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        9.17        40.21         9.21        35.24        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       18.15        28.73         0.69         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8682 TCGA-BR-8683 
        7.40         5.39         9.21        20.22        32.58         9.86 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       12.89         0.72        32.52        13.51        20.65         1.15 
TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 
       21.44        13.18        12.76        12.53        12.39        12.30 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4472 
       12.43        11.61        12.20        20.02         4.01        12.00 
TCGA-CG-4477 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 
       30.97         4.01        19.13        20.55        17.19        15.22 
TCGA-D7-6818 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 
       12.36        21.14        16.44        11.24        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
       19.96         0.62         7.99        72.23         3.48        19.53 
TCGA-FP-8099 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8610 
       17.06         1.51         5.92        28.96        22.32         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP 
       24.26        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 
        6.58        12.95        23.84        21.17        33.40         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 
        3.39        18.38         6.74         6.51        37.64        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
       18.21         6.08        11.05         8.61        16.67       122.30 
TCGA-VQ-A8DU TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.46        21.73         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N 
       17.85        64.57        14.33        39.45        21.83        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6I 
       32.88         1.71         9.50         9.04        21.04        16.14 
TCGA-VQ-AA6J 
       27.55 

$`AMP PEAK 21(10P11.22) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
       20.02        22.98        79.07        16.24        20.15        27.35 
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        35.21         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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        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-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-A88W 
       58.59         4.90        29.00         7.13        15.48        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.75         2.66        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76         5.49        21.37        13.41        83.24        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09        10.85         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.33        12.59        12.62        12.46        12.49        12.76 
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-LN-A8HZ TCGA-LN-A8I0 
       25.25        10.52        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 
        7.59        16.31         7.04        38.40         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
       15.35         8.98        25.81        22.82        12.43         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        18.18        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       15.91        25.08        41.23        14.37         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-4191 TCGA-BR-4201 
        9.44         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.56        29.42        19.96         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.05         3.72        25.18         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34         0.66         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       13.35        11.21        12.10        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43         6.31        11.31         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       54.08        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        18.97         7.07         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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.91        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        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       77.29        63.06        52.21        30.51        26.47        24.39 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       18.15        22.82        21.07        24.30         5.59        22.68 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
        3.25        21.37        29.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        29.00        23.80        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       36.36        18.81        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A8MW 
        8.52        74.53         4.60         9.24         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        13.02        18.48        43.36        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       37.22        30.97        34.29        16.31         2.50         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W 
       73.41        11.70        61.22        20.81        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        55.56         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        12.43        17.26         0.79 

  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE 
                           0.23                            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 
                          13.38                           14.04 
[1] "0.2 - 122.3 (13.4)" "0.0 - 116.4 (14.0)"
[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       5       12       38       28        67
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(10P11.22) MUTATED          26         8         28         22
  AMP PEAK 21(10P11.22) WILD-TYPE        61        20         67         50
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(10P11.22) MUTATED            8       15         2
  AMP PEAK 21(10P11.22) WILD-TYPE         38       34         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  STAGE I                                5                               5
  STAGE IA                               9                              12
  STAGE IB                               9                              38
  STAGE II                               5                              28
  STAGE IIA                             20                              67
  STAGE IIB                             26                              61
  STAGE III                              8                              20
  STAGE IIIA                            28                              67
  STAGE IIIB                            22                              50
  STAGE IIIC                             8                              38
  STAGE IV                              15                              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
  AMP PEAK 21(10P11.22) MUTATED      19  27  86  30
  AMP PEAK 21(10P11.22) WILD-TYPE    36 109 197  94
D21V4, multiclass
       clus
vv      AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  T0+T1                            19                              36
  T2                               27                             109
  T3                               86                             197
  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    56  53  26  25
  AMP PEAK 21(10P11.22) WILD-TYPE 151 134  72  71
D21V5, multiclass
    clus
vv   AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  N0                            56                             151
  N1                            53                             134
  N2                            26                              72
  N3                            25                              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED   137  12
  AMP PEAK 21(10P11.22) WILD-TYPE 387  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED    137   12
  AMP PEAK 21(10P11.22) WILD-TYPE  387   27
   clus
vv  AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  0                           137                             387
  1                            12                              27
[1] 2 2
[1] FALSE
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED    47 122
  AMP PEAK 21(10P11.22) WILD-TYPE 138 318
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED     47  122
  AMP PEAK 21(10P11.22) WILD-TYPE  138  318
        clus
vv       AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  FEMALE                            47                             138
  MALE                             122                             318
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED   121  35
  AMP PEAK 21(10P11.22) WILD-TYPE 324  84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED    121   35
  AMP PEAK 21(10P11.22) WILD-TYPE  324   84
     clus
vv    AMP PEAK 21(10P11.22) MUTATED AMP PEAK 21(10P11.22) WILD-TYPE
  NO                            121                             324
  YES                            35                              84
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(10P11.22) MUTATED      43                         6
  AMP PEAK 21(10P11.22) WILD-TYPE    91                        11
                                 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     101
  AMP PEAK 21(10P11.22) WILD-TYPE   291
D21V11, multiclass
                                           clus
vv                                          AMP PEAK 21(10P11.22) MUTATED
  ASIAN                                                                43
  BLACK OR AFRICAN AMERICAN                                             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               101
                                           clus
vv                                          AMP PEAK 21(10P11.22) WILD-TYPE
  ASIAN                                                                  91
  BLACK OR AFRICAN AMERICAN                                              11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 291
[1] 4 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, binary
                                 cls
clus                                0   1
  AMP PEAK 21(10P11.22) MUTATED     2 112
  AMP PEAK 21(10P11.22) WILD-TYPE   9 292
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(10P11.22) MUTATED      2  112
  AMP PEAK 21(10P11.22) WILD-TYPE    9  292
                        clus
vv                       AMP PEAK 21(10P11.22) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           112
                        clus
vv                       AMP PEAK 21(10P11.22) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             292
[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    67  56
  AMP PEAK 22(10Q22.2) WILD-TYPE 287 189
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                           123                            476 
  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                            56                            189 
$`AMP PEAK 22(10Q22.2) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A8PU 
       15.68         4.31        47.05        21.99        16.24        27.35 
TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FA 
       26.93        58.55         4.21         0.79       122.10        44.75 
TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A893 
        3.68        25.22        26.33        32.61         3.16         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-LN-A49L 
       55.50         2.66        12.92        16.47        10.36        10.45 
TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A7HX 
       13.41        13.15        12.59        13.25        12.76        12.23 
TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A6Y0 
       12.85         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        52.27        18.21        19.73 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 
        6.61        18.35         4.08        17.29        19.33        26.10 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8077 
        9.21        35.24        33.63        18.15        14.43         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8485 
       29.42         2.66        15.58         7.40        14.04         9.21 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD 
       32.58         9.86        12.89         0.72        32.52        20.65 
TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 
        1.15        13.18        12.76        12.39        15.39        20.02 
TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6818 
       19.07        30.97        69.04        20.55        18.84        12.36 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       12.33        18.21        16.44        11.24        11.31        20.32 
TCGA-D7-A74A TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8610 
       19.96        72.23         0.56         1.51        22.32         0.76 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H6 
       24.26        24.20         8.98         6.58        12.95        21.17 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU 
       33.40         3.45         3.39        19.53         6.44        11.70 
TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N9 
       18.21         9.24        11.05         8.61       122.30        35.61 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX 
       21.73        46.26        12.79         1.87        13.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A925 
       14.33        39.45        21.83        18.74        20.81         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-AA64 
        5.72        66.81        18.41 

$`AMP PEAK 22(10Q22.2) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       20.02        22.98        79.07         0.23        20.15         9.86 
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        35.21 
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-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-A6FD TCGA-JY-A6FG 
       14.86         4.67        14.50        12.16        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25         0.30        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-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.75        13.48        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R 
       10.85         5.92        12.66        12.43        12.33        13.38 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       15.35        12.62        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        12.85        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-A7HY 
        4.47        12.33        25.25        10.52        12.00        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       12.26        33.11         7.82        16.31         7.04        38.40 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
        9.30         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        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 
       33.70        18.18        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         2.66        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        13.68        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       36.16        35.84        39.78        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8078 
        9.07        29.56        33.21        37.25        11.44        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 
        6.28         7.53        26.73        24.79        31.96        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        13.51         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.35        11.21        12.10        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.33        12.30        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-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-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        12.00         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.91        19.13        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-D7-8570 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        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.44        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        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-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       28.96        22.82        21.07        24.30         5.59        22.68 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       23.84        23.80        14.07        15.68        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        12.46        13.35         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A7C1 
        8.52        74.53         6.08         4.60         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        5.46        13.25        13.02        18.48        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50         2.70        17.85         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91S 
       15.65        29.59        73.41        11.70        61.22        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P 
        9.04         2.01        55.43         6.58        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE 
                          0.56                           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 
                         15.58                          13.63 
[1] "0.6 - 122.3 (15.6)" "0.0 - 116.4 (13.6)"
[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        10
  AMP PEAK 22(10Q22.2) WILD-TYPE       6       14       41       25        77
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(10Q22.2) MUTATED          15         7         23         16
  AMP PEAK 22(10Q22.2) WILD-TYPE        72        21         72         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(10Q22.2) MUTATED            6       11         2
  AMP PEAK 22(10Q22.2) WILD-TYPE         40       38         2
D22V3, multiclass
            clus
vv           AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              7                             14
  STAGE IB                              6                             41
  STAGE II                              8                             25
  STAGE IIA                            10                             77
  STAGE IIB                            15                             72
  STAGE III                             7                             21
  STAGE IIIA                           23                             72
  STAGE IIIB                           16                             56
  STAGE IIIC                            6                             40
  STAGE IV                             11                             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 22(10Q22.2) MUTATED      16  20  60  23
  AMP PEAK 22(10Q22.2) WILD-TYPE    39 116 223 101
D22V4, multiclass
       clus
vv      AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  T0+T1                           16                             39
  T2                              20                            116
  T3                              60                            223
  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    40  34  25  20
  AMP PEAK 22(10Q22.2) WILD-TYPE 167 153  73  76
D22V5, multiclass
    clus
vv   AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  N0                           40                            167
  N1                           34                            153
  N2                           25                             73
  N3                           20                             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   104   6
  AMP PEAK 22(10Q22.2) WILD-TYPE 420  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED    104    6
  AMP PEAK 22(10Q22.2) WILD-TYPE  420   33
   clus
vv  AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  0                          104                            420
  1                            6                             33
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED    35  90
  AMP PEAK 22(10Q22.2) WILD-TYPE 150 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED     35   90
  AMP PEAK 22(10Q22.2) WILD-TYPE  150  350
        clus
vv       AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  FEMALE                           35                            150
  MALE                             90                            350
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED    87  28
  AMP PEAK 22(10Q22.2) WILD-TYPE 358  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED     87   28
  AMP PEAK 22(10Q22.2) WILD-TYPE  358   91
     clus
vv    AMP PEAK 22(10Q22.2) MUTATED AMP PEAK 22(10Q22.2) WILD-TYPE
  NO                            87                            358
  YES                           28                             91
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(10Q22.2) MUTATED      29                         1
  AMP PEAK 22(10Q22.2) WILD-TYPE   105                        16
                                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   310
D22V11, multiclass
                                           clus
vv                                          AMP PEAK 22(10Q22.2) MUTATED
  ASIAN                                                               29
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               82
                                           clus
vv                                          AMP PEAK 22(10Q22.2) WILD-TYPE
  ASIAN                                                                105
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D22V12, binary
                                cls
clus                               0   1
  AMP PEAK 22(10Q22.2) MUTATED     0  83
  AMP PEAK 22(10Q22.2) WILD-TYPE  11 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(10Q22.2) MUTATED      0   83
  AMP PEAK 22(10Q22.2) WILD-TYPE   11  321
                        clus
vv                       AMP PEAK 22(10Q22.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       AMP PEAK 22(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            321
[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    63  53
  AMP PEAK 23(10Q26.13) WILD-TYPE 291 192
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                            116                             483 
  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                             53                             192 
$`AMP PEAK 23(10Q26.13) MUTATED`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-IC-A6RE TCGA-IG-A4P3 
       15.68         4.31        26.93        58.55         7.69        18.64 
TCGA-IG-A5B8 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OO 
        0.79       122.10         3.68        25.22        26.33         3.32 
TCGA-L5-A4OR TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
        3.16         2.60         3.02        55.50         2.66        16.47 
TCGA-L7-A6VZ TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A4A3 TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.36        13.15        12.59        12.76         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-VR-A8EQ TCGA-VR-A8Q7 
        6.35        53.95        15.78         2.89        22.82        52.27 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4255 
       18.21        19.73         6.61         4.64        18.35         4.08 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 
       17.29        13.68        26.10        31.20         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       33.63        39.78         0.69         9.60        29.42         2.66 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PF 
       15.58         7.40        32.58         0.72        32.52         1.15 
TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 
       13.18        12.59         7.17        12.39        15.39        20.02 
TCGA-CG-4304 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       27.02        29.98        19.07         7.07        12.00        30.97 
TCGA-CG-5718 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 
       36.00         4.01        69.04        20.55        18.84        17.19 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV 
       15.22        12.36        16.80        14.27        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 
       11.31        20.32         0.62         7.99        72.23         3.48 
TCGA-FP-8099 TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 
       17.06         1.51        22.32         0.76        24.26        24.20 
TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP 
        0.26        23.80        21.17         3.39        18.38         6.44 
TCGA-KB-A6F5 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-VQ-A8DU TCGA-VQ-A8E0 
        5.56        18.21         6.08        11.05         5.46        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E 
       21.73        46.26        12.79        64.57        14.33        21.83 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 
       18.74        20.81        32.88         9.73         4.54         5.72 
TCGA-VQ-A92D TCGA-VQ-AA64 
       66.81        18.41 

$`AMP PEAK 23(10Q26.13) WILD-TYPE`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        34.85        18.28         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23        20.15         9.86        27.35        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        20.12         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-A97H 
       23.41        12.82         9.96        14.86         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75        68.02        41.52        47.38        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-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        32.61        21.01        47.93        18.35         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-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NI 
       15.48        25.12         7.40         3.75        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-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8WC 
        8.02        16.31         7.04        38.40         9.30         2.30 
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        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        27.09        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        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        9.44         6.97         7.43        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-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-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       19.96         2.20         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.33        12.30        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 
        6.58        12.20        11.77        12.62         3.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5719 
       12.03         0.00         9.01        18.97         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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.91        19.13        18.54        18.61        17.85        13.35 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       10.26        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8573 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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38        19.53        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       77.29        63.06        52.21        30.51        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       24.39        18.15        28.96        22.82        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        22.68         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 
       20.25         2.10        12.95        29.00        23.84        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
       15.68        33.40        36.36         3.45        18.81        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        15.75        13.51         2.53        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       36.95         3.72        19.73        14.04        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       74.53         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        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-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-A8PZ TCGA-VQ-A91A 
       23.41        15.65        13.35        29.59        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70        61.22         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O 
       55.56         9.04         2.01        55.43         6.58        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
        2.66        42.54        11.24        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE 
                           0.26                            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 
                         15.485                          13.580 
[1] "0.3 - 122.1 (15.5)" "0.0 - 122.3 (13.6)"
[1] "hr=" "1.2"
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       6       13       39       25        80
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(10Q26.13) MUTATED          15         6         23          9
  AMP PEAK 23(10Q26.13) WILD-TYPE        72        22         72         63
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(10Q26.13) MUTATED            8       10         2
  AMP PEAK 23(10Q26.13) WILD-TYPE         38       39         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  STAGE I                                4                               6
  STAGE IA                               8                              13
  STAGE IB                               8                              39
  STAGE II                               8                              25
  STAGE IIA                              7                              80
  STAGE IIB                             15                              72
  STAGE III                              6                              22
  STAGE IIIA                            23                              72
  STAGE IIIB                             9                              63
  STAGE IIIC                             8                              38
  STAGE IV                              10                              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
  AMP PEAK 23(10Q26.13) MUTATED      16  22  54  19
  AMP PEAK 23(10Q26.13) WILD-TYPE    39 114 229 105
D23V4, multiclass
       clus
vv      AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  T0+T1                            16                              39
  T2                               22                             114
  T3                               54                             229
  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 169 154  77  78
D23V5, multiclass
    clus
vv   AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  N0                            38                             169
  N1                            33                             154
  N2                            21                              77
  N3                            18                              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"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED    98   5
  AMP PEAK 23(10Q26.13) WILD-TYPE 426  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED     98    5
  AMP PEAK 23(10Q26.13) WILD-TYPE  426   34
   clus
vv  AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  0                            98                             426
  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 149 357
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED     36   83
  AMP PEAK 23(10Q26.13) WILD-TYPE  149  357
        clus
vv       AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  FEMALE                            36                             149
  MALE                              83                             357
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED    84  23
  AMP PEAK 23(10Q26.13) WILD-TYPE 361  96
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED     84   23
  AMP PEAK 23(10Q26.13) WILD-TYPE  361   96
     clus
vv    AMP PEAK 23(10Q26.13) MUTATED AMP PEAK 23(10Q26.13) WILD-TYPE
  NO                             84                             361
  YES                            23                              96
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(10Q26.13) MUTATED      19                         5
  AMP PEAK 23(10Q26.13) WILD-TYPE   115                        12
                                 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   313
D23V11, 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                                                                 115
  BLACK OR AFRICAN AMERICAN                                              12
  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"
D23V12, binary
                                 cls
clus                                0   1
  AMP PEAK 23(10Q26.13) MUTATED     0  75
  AMP PEAK 23(10Q26.13) WILD-TYPE  11 329
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(10Q26.13) MUTATED      0   75
  AMP PEAK 23(10Q26.13) WILD-TYPE   11  329
                        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                                  11
  NOT HISPANIC OR LATINO                             329
[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    69  62
  AMP PEAK 24(11P13) WILD-TYPE 285 183
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                         131                          468 
  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                          62                          183 
$`AMP PEAK 24(11P13) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-FP-A8CX TCGA-VQ-A8PU 
       18.28         8.94        24.00        27.12         0.23        27.35 
TCGA-VQ-A94U TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A50L TCGA-IG-A8O2 
       26.93         7.63         8.94        16.24         0.53         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A4OH TCGA-L5-A4OM 
       14.50       122.10         3.68        25.22        32.61        47.93 
TCGA-L5-A4ON TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NN 
       18.35         4.90        29.00        15.48         2.66         5.49 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V 
       52.57        46.09         5.92        12.33        13.15        12.59 
TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       12.59        22.39        12.33        13.22         4.47        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        12.03        12.33        13.38        12.85        12.26 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-RE-A7BO TCGA-V5-A7RC TCGA-VR-A8EQ 
        7.82         7.59         7.04         7.00         3.42        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-ZR-A9CJ TCGA-3M-AB46 
       12.43        18.31        28.11        18.18        19.73        58.03 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-6456 
       11.70        11.01         9.44         9.67        13.87        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
       19.33        26.10        18.15         3.45        11.44         0.69 
TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 
        9.60        15.58         7.40         9.21         9.34        24.79 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 
       20.88        34.13         6.08        34.98        12.89        14.17 
TCGA-BR-A4J8 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-A487 
       13.51        12.59        12.33        12.39        15.39        12.30 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-5717 
       12.20        20.02        54.08        19.07        12.00         6.97 
TCGA-CG-5722 TCGA-D7-6822 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7916 
        0.99        12.33        14.66         0.62         7.99        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4G2 
       17.06         0.56        63.06         5.92        28.96        24.30 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A7NT TCGA-IN-A7NU 
       33.40         3.45        18.38        12.46        10.62        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56        37.64        18.21        74.53         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
      115.69        57.44         5.46        13.02        18.48        43.36 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Y 
       22.19         2.70        64.57        32.88         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6K 
        9.04         4.54        32.94        54.12        12.43 

$`AMP PEAK 24(11P13) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        34.85         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
       22.82         0.36        35.97         5.16        20.02        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        79.07        16.24        20.15         9.86 
TCGA-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-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         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-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       12.16        44.75        68.02        41.52        47.38        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-A4OF TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
        0.30        26.33        21.01         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        3.16        58.59         7.13         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75         3.02        55.50        12.92        13.48 
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-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       13.41        83.24        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.43        13.41        13.38        15.35        13.25        12.62 
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        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I1 
       11.54        12.33        25.25        12.23        13.18        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        12.03        33.11         8.02         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV 
        2.30        12.69        20.38         5.29        16.44        15.35 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
        9.27         8.98        25.81        27.09         1.55         8.12 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
        2.10         1.32         2.66        26.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       34.68        15.95        13.68        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        39.78        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        29.56        33.21        37.25        14.43        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.20         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS 
        9.86         8.22        10.68        13.87         7.53         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 
       27.55        28.57         8.98         0.72         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
        7.17        12.30        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        7.99         8.05         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 
        0.00         9.01        18.97         7.07        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-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 
       25.71        12.66        20.91        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 
       15.65         8.38         4.34        19.96         7.13        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51        26.47         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07         0.76         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       23.80        21.17        14.07        15.68        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
        6.51        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        19.73        14.04        45.67         8.52         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.60         9.24        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38         8.94        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 
       19.04         5.79         0.92        48.79        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        16.31         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PY 
        9.27        23.41        15.65        13.35        29.59        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81         1.71        42.64        60.85        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        16.14        27.55        17.26         0.79 

  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE 
                        0.23                         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 
                       12.85                        14.35 
[1] "0.2 - 122.1 (12.8)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D24V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(11P13) MUTATED         3        4        8        4        18
  AMP PEAK 24(11P13) WILD-TYPE       7       17       39       29        69
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(11P13) MUTATED          20         8         18         15
  AMP PEAK 24(11P13) WILD-TYPE        67        20         77         57
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 24(11P13) MUTATED           12       16         3
  AMP PEAK 24(11P13) WILD-TYPE         34       33         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  STAGE I                             3                            7
  STAGE IA                            4                           17
  STAGE IB                            8                           39
  STAGE II                            4                           29
  STAGE IIA                          18                           69
  STAGE IIB                          20                           67
  STAGE III                           8                           20
  STAGE IIIA                         18                           77
  STAGE IIIB                         15                           57
  STAGE IIIC                         12                           34
  STAGE IV                           16                           33
  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  18  70  32
  AMP PEAK 24(11P13) WILD-TYPE    43 118 213  92
D24V4, multiclass
       clus
vv      AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  T0+T1                         12                           43
  T2                            18                          118
  T3                            70                          213
  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    39  45  25  20
  AMP PEAK 24(11P13) WILD-TYPE 168 142  73  76
D24V5, multiclass
    clus
vv   AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  N0                         39                          168
  N1                         45                          142
  N2                         25                           73
  N3                         20                           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"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED   108  13
  AMP PEAK 24(11P13) WILD-TYPE 416  26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED    108   13
  AMP PEAK 24(11P13) WILD-TYPE  416   26
   clus
vv  AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  0                        108                          416
  1                         13                           26
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED    30 108
  AMP PEAK 24(11P13) WILD-TYPE 155 332
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED     30  108
  AMP PEAK 24(11P13) WILD-TYPE  155  332
        clus
vv       AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  FEMALE                         30                          155
  MALE                          108                          332
[1] 2 2
[1] FALSE
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED    92  31
  AMP PEAK 24(11P13) WILD-TYPE 353  88
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED     92   31
  AMP PEAK 24(11P13) WILD-TYPE  353   88
     clus
vv    AMP PEAK 24(11P13) MUTATED AMP PEAK 24(11P13) WILD-TYPE
  NO                          92                          353
  YES                         31                           88
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(11P13) MUTATED      37                         4
  AMP PEAK 24(11P13) WILD-TYPE    97                        13
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 24(11P13) MUTATED                                           1    78
  AMP PEAK 24(11P13) WILD-TYPE                                         0   314
D24V11, multiclass
                                           clus
vv                                          AMP PEAK 24(11P13) MUTATED
  ASIAN                                                             37
  BLACK OR AFRICAN AMERICAN                                          4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             78
                                           clus
vv                                          AMP PEAK 24(11P13) WILD-TYPE
  ASIAN                                                               97
  BLACK OR AFRICAN AMERICAN                                           13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  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"
D24V12, binary
                              cls
clus                             0   1
  AMP PEAK 24(11P13) MUTATED     2  84
  AMP PEAK 24(11P13) WILD-TYPE   9 320
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(11P13) MUTATED      2   84
  AMP PEAK 24(11P13) WILD-TYPE    9  320
                        clus
vv                       AMP PEAK 24(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       AMP PEAK 24(11P13) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          320
[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   126  82
  AMP PEAK 25(11Q13.3) WILD-TYPE 228 163
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                           208                            391 
  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                            82                            163 
$`AMP PEAK 25(11Q13.3) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       60.39        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A88Y TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GN 
        4.70         0.36        47.05         9.86        27.35         8.94 
TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D 
       33.27         0.85        20.78        20.12        18.64        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 
       23.41         9.96         4.67        14.50        12.16       122.10 
TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM 
        3.68        25.22         0.30        26.33        32.61        47.93 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        1.38        58.59        29.00        15.48         2.60         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NN 
       55.50         2.66        12.92        13.48        13.55         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       21.37         8.71        52.57        46.09        10.85         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X 
       12.66        12.43        13.38        13.15        13.25        12.62 
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-A5U6 TCGA-LN-A5U7 
       12.85        15.52        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        12.33        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.03        12.26         7.82         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-V5-A7RC 
        7.04         6.35        53.95        15.78         7.00         3.42 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        9.27        25.81        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-AA7B 
       28.11        33.70        18.18        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.10         1.32         2.66        19.73        11.01         9.44 
TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7901 
        9.67        13.87        13.68        35.24        18.15         3.45 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8365 
       37.25         0.69         9.60        15.58        31.10        17.52 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4CQ 
        9.21        27.12        24.79        20.88         8.22        34.98 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8525 
        1.48        12.89         1.15        21.44        13.02        12.59 
TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 
       12.33        11.64        15.39        12.07        12.82        12.30 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 
       11.61        12.20        20.02        54.08        19.07        12.03 
TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EV 
       12.00         0.99        12.03        18.21        14.66        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 
       22.29        15.65         7.99        72.23        17.06         0.56 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4GC 
       63.06        52.21         5.92         0.76        24.30         3.25 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        0.26        23.84        23.80        21.17        33.40         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       12.46        13.35         6.44         6.74        10.62        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        5.56        37.64        74.53         8.61        16.67       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8DU 
      115.69        57.44         8.94        35.61        19.04         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PX 
       13.02        18.48        43.36        22.19         2.70        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U 
       14.33        39.45        21.83        18.74        32.88         1.71 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
        9.73         4.54        66.81        11.24        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        27.55        12.43         0.79 

$`AMP PEAK 25(11Q13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       15.68        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.15        26.93        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        7.69        35.21         2.63         3.88         9.30         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        0.79        12.82        14.86        44.75        68.02        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        3.16        30.25        21.01        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        3.16         4.90         7.13         7.43        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NS TCGA-L5-A8NU 
        3.02        16.47        13.22         7.76        13.41        83.24 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V 
       10.36        10.45        13.41        12.33        15.35        12.59 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-M9-A5M8 
       11.54         4.47        10.52        13.38        12.85        33.11 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06        16.31        38.40         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX 
       12.69        20.38         5.29        16.44        15.35         8.98 
TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-3M-AB46 TCGA-B7-5816 
       27.09         1.55        52.27        18.21        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        19.56         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 
        6.18         9.57         6.61        34.68        15.95        17.29 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       19.33        39.12        26.10         9.17        32.78        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       33.63        39.78        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       33.21        14.43        11.44        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        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        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         3.72         5.39        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T 
       26.73        31.96        32.58         9.86        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       13.87         7.53         6.08        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.76        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43         6.31        11.31        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 
        8.05         4.01        14.01        29.98         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       20.91        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        36.43        13.78        14.76        26.43        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        14.47        21.27        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       14.07        22.29        59.54         5.03        13.58         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
        6.21        77.29        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 
       18.15        28.96        22.32        22.82        21.07         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         2.10        12.95        29.00        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RS 
       36.36         3.45        18.81        18.38        19.53        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
        6.51        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        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        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        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        29.59        73.41        11.70        61.22        20.81 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64        60.85         9.50        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        21.04         2.66        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        17.13        54.12        26.04        16.14 
TCGA-ZA-A8F6 
       17.26 

  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE 
                          0.13                           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 
                        13.085                         14.760 
[1] "0.1 - 122.3 (13.1)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(11Q13.3) MUTATED         4        7       10        9        36
  AMP PEAK 25(11Q13.3) WILD-TYPE       6       14       37       24        51
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(11Q13.3) MUTATED          31        16         30         24
  AMP PEAK 25(11Q13.3) WILD-TYPE        56        12         65         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 25(11Q13.3) MUTATED           17       15         3
  AMP PEAK 25(11Q13.3) WILD-TYPE         29       34         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              7                             14
  STAGE IB                             10                             37
  STAGE II                              9                             24
  STAGE IIA                            36                             51
  STAGE IIB                            31                             56
  STAGE III                            16                             12
  STAGE IIIA                           30                             65
  STAGE IIIB                           24                             48
  STAGE IIIC                           17                             29
  STAGE IV                             15                             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 25(11Q13.3) MUTATED      21  47  97  41
  AMP PEAK 25(11Q13.3) WILD-TYPE    34  89 186  83
D25V4, multiclass
       clus
vv      AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  T0+T1                           21                             34
  T2                              47                             89
  T3                              97                            186
  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    73  68  38  24
  AMP PEAK 25(11Q13.3) WILD-TYPE 134 119  60  72
D25V5, multiclass
    clus
vv   AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  N0                           73                            134
  N1                           68                            119
  N2                           38                             60
  N3                           24                             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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED   183  11
  AMP PEAK 25(11Q13.3) WILD-TYPE 341  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED    183   11
  AMP PEAK 25(11Q13.3) WILD-TYPE  341   28
   clus
vv  AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  0                          183                            341
  1                           11                             28
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED    54 164
  AMP PEAK 25(11Q13.3) WILD-TYPE 131 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED     54  164
  AMP PEAK 25(11Q13.3) WILD-TYPE  131  276
        clus
vv       AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  FEMALE                           54                            131
  MALE                            164                            276
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED   146  51
  AMP PEAK 25(11Q13.3) WILD-TYPE 299  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED    146   51
  AMP PEAK 25(11Q13.3) WILD-TYPE  299   68
     clus
vv    AMP PEAK 25(11Q13.3) MUTATED AMP PEAK 25(11Q13.3) WILD-TYPE
  NO                           146                            299
  YES                           51                             68
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(11Q13.3) MUTATED      57                         9
  AMP PEAK 25(11Q13.3) WILD-TYPE    77                         8
                                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     128
  AMP PEAK 25(11Q13.3) WILD-TYPE   264
D25V11, multiclass
                                           clus
vv                                          AMP PEAK 25(11Q13.3) MUTATED
  ASIAN                                                               57
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              128
                                           clus
vv                                          AMP PEAK 25(11Q13.3) WILD-TYPE
  ASIAN                                                                 77
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  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"
D25V12, binary
                                cls
clus                               0   1
  AMP PEAK 25(11Q13.3) MUTATED     4 131
  AMP PEAK 25(11Q13.3) WILD-TYPE   7 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11Q13.3) MUTATED      4  131
  AMP PEAK 25(11Q13.3) WILD-TYPE    7  273
                        clus
vv                       AMP PEAK 25(11Q13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       AMP PEAK 25(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            273
[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   121  79
  AMP PEAK 26(12P12.1) WILD-TYPE 233 166
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                           200                            399 
  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                            79                            166 
$`AMP PEAK 26(12P12.1) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV 
        4.31        24.00        19.99         0.36        27.12        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GK TCGA-2H-A9GL 
       47.05        21.99        79.07        16.24         7.63         5.92 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC 
       16.24         4.21        32.45        35.21         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93D 
       18.64         3.88         0.53        23.41        14.50        31.56 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU 
        0.30        47.93        18.35         3.32         4.90        29.00 
TCGA-L5-A88S TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NW 
       15.48         2.66        16.47        13.22        21.37        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       10.85        10.36         5.92        10.45        12.66        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       12.33        13.38        13.15        12.59        13.25        12.59 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U5 
       12.76        12.59        12.85        15.52        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        25.25        10.52        12.00        13.18        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       13.18         0.13         8.02         7.59         5.06        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8ET 
        6.35        53.95        12.69        20.38        27.09         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-XP-A8T8 
       18.31         8.12        28.11        18.18        18.21        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-A5TK 
        3.42         2.10         1.32         2.66        19.73         9.47 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 
        6.61         4.08        39.12        32.78        25.61        12.16 
TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 
       40.21        28.73         3.45        33.21        29.59         2.20 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8369 
        7.40        31.10        13.08         0.26         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8687 
        3.32         7.36        20.22        27.12        24.79         8.22 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4PF 
        7.53        34.98         1.48         0.72        14.17         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.41        13.02        13.35        12.76        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 TCGA-CG-4472 
       12.39        12.59        12.43        11.61        20.02        12.00 
TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        0.99        12.03        12.66        19.13        20.55        18.54 
TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YV 
       17.19        12.79        11.31        19.50        18.21         5.92 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 
       11.31        22.29        15.65         8.38        19.96         0.62 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM 
       11.38         3.48        19.53        22.29         5.52         6.21 
TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD 
        1.51        28.96        22.82        24.30         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HB 
       25.81         8.98         6.51         6.58        20.25        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR 
       33.40         3.45         3.39        12.46         6.44         6.74 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.51        11.70        15.75         2.53        63.62        37.64 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N6 
       18.21        74.53         6.08        11.05        16.67         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.25        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91A 
       21.73         7.73        22.19        17.85        14.33        39.45 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A928 
       21.83        18.74        20.81        42.64         4.54         5.72 
TCGA-VQ-A94T TCGA-VQ-AA6K 
       11.24        12.43 

$`AMP PEAK 26(12P12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       22.82        35.97         5.16        22.98         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        9.86        27.35        26.93        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
       58.55        13.94         8.94         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.78         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
       14.86         4.67        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        23.18        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25        26.33        32.61 
TCGA-L5-A4OJ TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
       21.01         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50        12.92        13.48        13.55         7.76         5.49 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49U 
        8.71        13.41        83.24        52.57        12.43        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.62        12.46        12.49        22.39        11.54        12.33 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.23        12.03        13.38        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W5 
       33.11         7.82        16.31         7.04         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       15.91        25.08        41.23        58.03        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-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 
       13.68        19.33        26.10         9.17        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
       15.32         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8365 
        2.66        19.96        15.58         6.18        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
       26.33         4.31        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 
        6.08        27.55        28.57        12.89         8.98         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 
       20.42        21.44        16.14         5.13        13.15        13.18 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
       11.21        12.10        12.59        12.33        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.31         6.58        12.20        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-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-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         6.02       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.91        18.84        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.22        15.98        12.36        12.33        24.72        16.80 
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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       20.32         4.34         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       21.27        14.07        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        0.56        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        24.39        18.15        22.32        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ 
        5.59        24.26        22.68        24.20        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
       29.98         0.10         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-8462 
       23.84        23.80        21.17        14.07        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X 
       18.38        13.35        19.53        12.59        10.62        13.51 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
        5.56        36.95         3.72        19.73        14.04        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        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        64.57        73.41        11.70 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       61.22        32.88         1.71        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
       55.56         9.04         2.01        55.43         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       21.04         2.66        42.54        18.41        43.66        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE 
                          0.13                           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 
                        12.935                         15.020 
[1] "0.1 - 79.1 (12.9)"  "0.0 - 122.3 (15.0)"
[1] "hr=" "1.2"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(12P12.1) MUTATED         0        4       12        8        38
  AMP PEAK 26(12P12.1) WILD-TYPE      10       17       35       25        49
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(12P12.1) MUTATED          25        11         35         24
  AMP PEAK 26(12P12.1) WILD-TYPE        62        17         60         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 26(12P12.1) MUTATED           16       15         3
  AMP PEAK 26(12P12.1) WILD-TYPE         30       34         1
D26V3, multiclass
            clus
vv           AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  STAGE I                               0                             10
  STAGE IA                              4                             17
  STAGE IB                             12                             35
  STAGE II                              8                             25
  STAGE IIA                            38                             49
  STAGE IIB                            25                             62
  STAGE III                            11                             17
  STAGE IIIA                           35                             60
  STAGE IIIB                           24                             48
  STAGE IIIC                           16                             30
  STAGE IV                             15                             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 26(12P12.1) MUTATED      14  40 115  29
  AMP PEAK 26(12P12.1) WILD-TYPE    41  96 168  95
D26V4, multiclass
       clus
vv      AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  T0+T1                           14                             41
  T2                              40                             96
  T3                             115                            168
  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    66  62  36  32
  AMP PEAK 26(12P12.1) WILD-TYPE 141 125  62  64
D26V5, multiclass
    clus
vv   AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  N0                           66                            141
  N1                           62                            125
  N2                           36                             62
  N3                           32                             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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED   169  14
  AMP PEAK 26(12P12.1) WILD-TYPE 355  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED    169   14
  AMP PEAK 26(12P12.1) WILD-TYPE  355   25
   clus
vv  AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  0                          169                            355
  1                           14                             25
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED    50 157
  AMP PEAK 26(12P12.1) WILD-TYPE 135 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED     50  157
  AMP PEAK 26(12P12.1) WILD-TYPE  135  283
        clus
vv       AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  FEMALE                           50                            135
  MALE                            157                            283
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED   144  46
  AMP PEAK 26(12P12.1) WILD-TYPE 301  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED    144   46
  AMP PEAK 26(12P12.1) WILD-TYPE  301   73
     clus
vv    AMP PEAK 26(12P12.1) MUTATED AMP PEAK 26(12P12.1) WILD-TYPE
  NO                           144                            301
  YES                           46                             73
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(12P12.1) MUTATED      56                         5
  AMP PEAK 26(12P12.1) WILD-TYPE    78                        12
                                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     125
  AMP PEAK 26(12P12.1) WILD-TYPE   267
D26V11, multiclass
                                           clus
vv                                          AMP PEAK 26(12P12.1) MUTATED
  ASIAN                                                               56
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              125
                                           clus
vv                                          AMP PEAK 26(12P12.1) WILD-TYPE
  ASIAN                                                                 78
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D26V12, binary
                                cls
clus                               0   1
  AMP PEAK 26(12P12.1) MUTATED     4 143
  AMP PEAK 26(12P12.1) WILD-TYPE   7 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(12P12.1) MUTATED      4  143
  AMP PEAK 26(12P12.1) WILD-TYPE    7  261
                        clus
vv                       AMP PEAK 26(12P12.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       AMP PEAK 26(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            261
[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    92  64
  AMP PEAK 27(12Q15) WILD-TYPE 262 181
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                         156                          443 
  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                          64                          181 
$`AMP PEAK 27(12Q15) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 
        4.31         8.94        24.00        27.12        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR 
       22.98        79.07         0.23         7.63        16.24        32.45 
TCGA-IG-A50L TCGA-IG-A8O2 TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A88S 
        0.53         4.67        47.93         3.32         4.90        15.48 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NV 
       55.50         2.66        13.48        13.22         5.49        52.57 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       46.09        10.36        10.45        12.59        13.25        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6XG 
       12.33        13.18         0.13        12.26         7.59        38.40 
TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EP TCGA-VR-A8ET 
        6.35        12.69        20.38         3.42        27.09         1.55 
TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-Z6-A8JE 
       28.11        18.18        52.27        11.24        18.21         2.10 
TCGA-ZR-A9CJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6563 
       19.73         9.47         6.61        18.35         6.18        39.12 
TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       32.78        40.21        28.73        33.21        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8366 
       29.59         2.66         2.20         7.40         0.26         0.95 
TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-8687 
        3.32         7.36        25.18        27.12        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 
       34.13         7.53        34.98         1.48         0.72         0.53 
TCGA-BR-A4J6 TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8526 
        0.66         1.15        13.41        13.02        13.35        12.53 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4301 
       12.39        12.59        12.82        12.30        12.43         3.02 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       12.03        12.00         0.99        15.02        69.04        12.66 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       19.13        20.55        18.54        17.19        10.26        12.79 
TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 
       19.50         5.92        15.65         8.38        19.96         0.62 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8238 
       11.38        14.07        22.29         5.52         6.21         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT 
       28.96        22.82        24.30        22.75         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
        6.58        20.25        23.84        33.40         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-R5-A7ZI 
       12.46        19.53         6.44        15.75        63.62        74.53 
TCGA-R5-A7ZR TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        6.08         5.13        16.67        18.48        43.36         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91E 
       22.19        12.79         2.70        13.35        14.33        21.83 
TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA6K 
       20.81         9.50         9.04         4.54         5.72        12.43 

$`AMP PEAK 27(12Q15) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-EQ-A4SO 
       22.82         0.36        35.97         5.16        20.02        16.24 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ 
       14.30        58.55         5.92        13.94         8.94         4.21 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        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-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
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-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        3.16        30.25         0.30        26.33        32.61        21.01 
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-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ 
        3.02        12.92        16.47        13.55         7.76        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
        8.71        13.41        83.24        10.85         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MR 
       12.62        12.46        12.49        12.76        22.39        13.22 
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-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        13.38        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         5.06        16.31         7.04        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.89         2.30         7.00         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       18.31         8.12        33.70        46.19        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        25.08        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.44         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.87        17.29        13.68        19.33        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
        3.45         9.07        29.56        37.25        14.43         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       32.25         8.05         0.56        29.42        19.96        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        31.10        13.08        22.19        17.52        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 
        4.31        14.04        11.80        31.27        14.79        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A453 
       31.96        32.58         9.86        10.68        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
       27.55        28.57        12.89         8.98        14.17        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       32.52        13.51         0.46        20.65        20.42        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 
       16.14         5.13        13.15        13.18        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
       12.76        12.59         7.17        12.33        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C 
       15.39        12.07        12.43         6.31        11.31        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        6.58        12.20        11.77        12.62        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-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-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         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-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02       105.07        12.03        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 
       21.07         7.99        25.71        20.91        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        15.22        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        17.19        18.21        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       22.29         4.34         7.13         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       21.27         3.48        19.53        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       13.58         0.56        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GY 
       25.81        11.77        21.37        29.98         0.10         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
       15.68        36.36        18.81        18.38        13.35         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67        18.21         8.52         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.50        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.73        55.56         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        17.26         0.79 

  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE 
                        0.13                         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 
                       12.59                        14.86 
[1] "0.1 - 79.1 (12.6)"  "0.0 - 122.3 (14.9)"
[1] "hr=" "1.2"
D27V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(12Q15) MUTATED         0        4       11        8        25
  AMP PEAK 27(12Q15) WILD-TYPE      10       17       36       25        62
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(12Q15) MUTATED          18         8         25         16
  AMP PEAK 27(12Q15) WILD-TYPE        69        20         70         56
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 27(12Q15) MUTATED           13       17         3
  AMP PEAK 27(12Q15) WILD-TYPE         33       32         1
D27V3, multiclass
            clus
vv           AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  STAGE I                             0                           10
  STAGE IA                            4                           17
  STAGE IB                           11                           36
  STAGE II                            8                           25
  STAGE IIA                          25                           62
  STAGE IIB                          18                           69
  STAGE III                           8                           20
  STAGE IIIA                         25                           70
  STAGE IIIB                         16                           56
  STAGE IIIC                         13                           33
  STAGE IV                           17                           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 27(12Q15) MUTATED      11  32  80  32
  AMP PEAK 27(12Q15) WILD-TYPE    44 104 203  92
D27V4, multiclass
       clus
vv      AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  T0+T1                         11                           44
  T2                            32                          104
  T3                            80                          203
  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    47  53  30  24
  AMP PEAK 27(12Q15) WILD-TYPE 160 134  68  72
D27V5, multiclass
    clus
vv   AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  N0                         47                          160
  N1                         53                          134
  N2                         30                           68
  N3                         24                           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   128  15
  AMP PEAK 27(12Q15) WILD-TYPE 396  24
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED    128   15
  AMP PEAK 27(12Q15) WILD-TYPE  396   24
   clus
vv  AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  0                        128                          396
  1                         15                           24
[1] 2 2
[1] FALSE
D27V7, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED    41 120
  AMP PEAK 27(12Q15) WILD-TYPE 144 320
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED     41  120
  AMP PEAK 27(12Q15) WILD-TYPE  144  320
        clus
vv       AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  FEMALE                         41                          144
  MALE                          120                          320
[1] 2 2
[1] FALSE
D27V8, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED   114  32
  AMP PEAK 27(12Q15) WILD-TYPE 331  87
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED    114   32
  AMP PEAK 27(12Q15) WILD-TYPE  331   87
     clus
vv    AMP PEAK 27(12Q15) MUTATED AMP PEAK 27(12Q15) WILD-TYPE
  NO                         114                          331
  YES                         32                           87
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(12Q15) MUTATED      44                         3
  AMP PEAK 27(12Q15) WILD-TYPE    90                        14
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 27(12Q15) MUTATED                                           0    93
  AMP PEAK 27(12Q15) WILD-TYPE                                         1   299
D27V11, multiclass
                                           clus
vv                                          AMP PEAK 27(12Q15) MUTATED
  ASIAN                                                             44
  BLACK OR AFRICAN AMERICAN                                          3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             93
                                           clus
vv                                          AMP PEAK 27(12Q15) WILD-TYPE
  ASIAN                                                               90
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  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"
D27V12, binary
                              cls
clus                             0   1
  AMP PEAK 27(12Q15) MUTATED     3 105
  AMP PEAK 27(12Q15) WILD-TYPE   8 299
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 27(12Q15) MUTATED      3  105
  AMP PEAK 27(12Q15) WILD-TYPE    8  299
                        clus
vv                       AMP PEAK 27(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        105
                        clus
vv                       AMP PEAK 27(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          299
[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  81
  AMP PEAK 28(13Q12.3) WILD-TYPE 229 164
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                           206                            393 
  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                            81                            164 
$`AMP PEAK 28(13Q12.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT 
       18.28         8.94         4.70        19.99         0.36        27.12 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       20.02        47.05        79.07         9.86        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YB 
       14.30         5.92        13.94        32.45         7.69         2.63 
TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E 
        0.79        14.50        47.38        31.56         3.16        30.25 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 
        7.17         1.38         4.90         7.13         2.60         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 
       55.50         2.66        12.92        25.25        12.00        13.18 
TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W5 
       12.85         7.82        16.31         7.04        53.95        15.78 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29         3.42         9.27        33.70        46.19        18.21 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4187 
       19.73        58.03        11.70        11.01         9.44         4.64 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6565 
        9.67         9.57         6.61        15.95        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7717 
       32.78        25.61        40.21         9.21        35.24        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       28.73         3.45        11.44         0.69        29.59         9.60 
TCGA-BR-8286 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 
       29.42        13.08        14.79        25.05         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       20.22        12.79        32.58        20.88         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 
       13.87        34.98         0.72        14.17        28.34        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 
        0.46        20.65        20.42         1.15         5.13        13.02 
TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8535 
       13.15        12.10        12.59         7.17        12.33        12.82 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
        6.31        12.43         6.58        12.20        20.02         3.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-4472 
       15.95         7.99         8.05        54.08         7.07        12.00 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
        1.02        12.03         4.01        69.04         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6815 
       12.66        19.13        18.54        17.85        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.79        12.36        11.31        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 
       21.14        14.27        14.76        11.24        22.29        15.65 
TCGA-D7-A747 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        8.38         0.62         7.99        72.23         3.48        19.53 
TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8245 TCGA-HU-8249 
       17.06         5.52        63.06        52.21        18.15        28.96 
TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT 
       22.82        24.26        22.68        22.75        25.81         6.51 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
        0.26        29.00        23.84        23.80        33.40         3.45 
TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       18.38         6.44        12.59        11.70         5.56        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BT TCGA-RD-A8MV 
       14.04        45.67        18.21         8.52         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       48.79         5.46        13.25        13.02        21.73        37.41 
TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PY 
        7.73        22.19         2.70        17.85        23.41        14.33 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91Z 
       39.45        20.81        32.88         1.71        42.64        55.56 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6B TCGA-VQ-AA6J 
        9.04        21.04        42.54        11.24        32.94        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`AMP PEAK 28(13Q12.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A88T 
       15.68        60.39        34.85         4.31        24.00        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX 
       35.97         5.16        21.99        22.98        16.24         0.23 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN 
       20.15        27.35        26.93        58.55         7.63         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       16.24         4.21        33.27        35.21         0.85        20.78 
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-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF 
       23.18        25.22        24.03         6.28         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
       32.61        21.01        47.93        18.35         3.32         3.16 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        3.75        13.48        16.47        13.55        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-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       46.09        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        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        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.33        13.22         4.47        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.03        13.18        12.33        13.38         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       12.26        33.11         8.02         7.59         5.06        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38        16.44        15.35         8.98        25.81        27.09 
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-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
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-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18        34.68        13.87        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       26.10        18.05        19.89        12.16         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        44.94        21.90        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       39.78        15.32         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       14.43        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 
        3.32        11.80        31.27         7.36         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 
       26.73        24.79        31.96         9.86        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.53         0.66        32.52        21.44        16.14        13.41 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 
       13.18        13.35        11.21        12.76        12.53        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.39        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 
       12.30        11.31        11.61        11.77        12.62        27.02 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        1.02         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        18.97        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       65.10        21.07        20.91        20.55        18.84        18.61 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       13.35        10.26        15.22        12.33        24.72        16.80 
TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       26.43        11.31        11.44        20.32         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        7.13        14.47        21.27        11.38        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       30.51        26.47         1.51         5.92        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76        24.30         5.59        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         2.10        12.95        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74         6.51        10.62        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62        36.95         3.72        19.73        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 
        4.60         9.24        11.05         5.13        16.67        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 
      116.38        71.38        16.87        19.04         0.92        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       43.36        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.50        12.79         1.87         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        29.59        64.57        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
       61.22        18.74        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        28.41        38.93        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       26.04        16.14        17.26 

  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE 
                          0.26                           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 
                        14.105                         13.780 
[1] "0.3 - 122.3 (14.1)" "0.0 - 122.1 (13.8)"
[1] "hr=" "1.1"
D28V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(13Q12.3) MUTATED         4        7       12       12        25
  AMP PEAK 28(13Q12.3) WILD-TYPE       6       14       35       21        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(13Q12.3) MUTATED          30         5         36         24
  AMP PEAK 28(13Q12.3) WILD-TYPE        57        23         59         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 28(13Q12.3) MUTATED           15       23         2
  AMP PEAK 28(13Q12.3) WILD-TYPE         31       26         2
D28V3, multiclass
            clus
vv           AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              7                             14
  STAGE IB                             12                             35
  STAGE II                             12                             21
  STAGE IIA                            25                             62
  STAGE IIB                            30                             57
  STAGE III                             5                             23
  STAGE IIIA                           36                             59
  STAGE IIIB                           24                             48
  STAGE IIIC                           15                             31
  STAGE IV                             23                             26
  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  49  93  43
  AMP PEAK 28(13Q12.3) WILD-TYPE    35  87 190  81
D28V4, multiclass
       clus
vv      AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  T0+T1                           20                             35
  T2                              49                             87
  T3                              93                            190
  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    62  61  37  40
  AMP PEAK 28(13Q12.3) WILD-TYPE 145 126  61  56
D28V5, multiclass
    clus
vv   AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  N0                           62                            145
  N1                           61                            126
  N2                           37                             61
  N3                           40                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED   176  16
  AMP PEAK 28(13Q12.3) WILD-TYPE 348  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED    176   16
  AMP PEAK 28(13Q12.3) WILD-TYPE  348   23
   clus
vv  AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  0                          176                            348
  1                           16                             23
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED    63 153
  AMP PEAK 28(13Q12.3) WILD-TYPE 122 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED     63  153
  AMP PEAK 28(13Q12.3) WILD-TYPE  122  287
        clus
vv       AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  FEMALE                           63                            122
  MALE                            153                            287
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED   158  37
  AMP PEAK 28(13Q12.3) WILD-TYPE 287  82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED    158   37
  AMP PEAK 28(13Q12.3) WILD-TYPE  287   82
     clus
vv    AMP PEAK 28(13Q12.3) MUTATED AMP PEAK 28(13Q12.3) WILD-TYPE
  NO                           158                            287
  YES                           37                             82
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(13Q12.3) MUTATED      38                         8
  AMP PEAK 28(13Q12.3) WILD-TYPE    96                         9
                                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     133
  AMP PEAK 28(13Q12.3) WILD-TYPE   259
D28V11, multiclass
                                           clus
vv                                          AMP PEAK 28(13Q12.3) MUTATED
  ASIAN                                                               38
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              133
                                           clus
vv                                          AMP PEAK 28(13Q12.3) WILD-TYPE
  ASIAN                                                                 96
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                259
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK 28(13Q12.3) MUTATED     3 140
  AMP PEAK 28(13Q12.3) WILD-TYPE   8 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(13Q12.3) MUTATED      3  140
  AMP PEAK 28(13Q12.3) WILD-TYPE    8  264
                        clus
vv                       AMP PEAK 28(13Q12.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          140
                        clus
vv                       AMP PEAK 28(13Q12.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            264
[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   144  89
  AMP PEAK 29(13Q22.1) WILD-TYPE 210 156
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                           233                            366 
  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                            89                            156 
$`AMP PEAK 29(13Q22.1) MUTATED`
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y TCGA-L5-A8NT TCGA-S8-A6BV 
        8.94         4.70        19.99         0.36        27.12        20.02 
TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
        9.86        31.27        14.30         5.92        13.94         4.21 
TCGA-IC-A6RE TCGA-IG-A5B8 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FH 
        7.69         0.79        14.50       122.10         3.68        47.38 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OP TCGA-L5-A4OQ 
       23.18        31.56         3.16        30.25         7.17         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       58.59         7.13        15.48         3.02         2.66        12.92 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NW TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49U 
        8.71        13.41        46.09        10.45        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U7 
       12.59        12.59        12.59        12.85        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
       12.00        12.23        12.85         7.82         8.02        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
        7.04        38.40        53.95         9.30        15.78        12.69 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-AA4D TCGA-X8-AAAR 
        5.29         3.42         9.27        27.09        46.19        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ 
       25.08        14.37        19.73        58.03        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 
        9.44         4.64         7.43         9.67         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        40.21         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       35.24        33.63        39.78        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        29.59         9.60        13.08        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8678 TCGA-BR-8682 
       25.05         5.39         9.21        12.79        24.79        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY 
       20.88         8.22        10.68        13.87        34.98        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.72        14.17        28.34        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        13.02        13.15        13.35 
TCGA-CD-8525 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
       12.59        15.39        12.82         6.31        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 
       25.71        12.66        20.91        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        12.36        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        22.29 
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-HF-7134 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
        0.56         5.52        52.21        18.15        28.96        22.82 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU 
       24.26        22.68        22.75        25.81         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 
        0.26        29.00        23.84        23.80        33.40         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IP-7968 
       18.38        13.35         6.44         6.51        11.70         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        5.56        37.64        14.04        45.67        18.21         8.52 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61       122.30        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61         5.79        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36        21.73        37.41        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 
       32.88         1.71        42.64         9.50        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 
        4.54        66.81        21.04        42.54        11.24        43.66 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        26.04        27.55        12.43 

$`AMP PEAK 29(13Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       22.82        35.97         5.16        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07        16.24         0.23        20.15        27.35        26.93 
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-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       33.27        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       18.64         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-A6FA 
       12.82         9.96        14.86         4.67        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       68.02        41.52        21.70        25.22        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        0.30        26.33        32.61        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88V 
        3.32         3.16         4.90        29.00         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40         3.75        55.50        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49        21.37        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       52.57        10.85        10.36         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.41        12.33        13.15        13.25        12.62        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.49        12.76        22.39        15.52        11.54        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
        4.47        12.33        10.52        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.03        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        7.59         5.06         6.35         2.89         2.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ 
       20.38        16.44        15.35         8.98        25.81        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        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       41.23         3.42         2.10         1.32         2.66        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 
       19.56         9.47         6.61         6.97        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 
        4.08         4.08         9.34         6.18        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       17.29        13.68        19.33        26.10        25.61        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        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 
       21.90        36.16        35.84        15.32         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 
       33.21        37.25        14.43        11.44        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         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-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
       31.27         3.72        25.18        20.22         1.12        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        9.86        34.13         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QI 
       28.57         8.98         0.53         0.66        32.52        21.44 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       16.14        13.41        13.18        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       11.64        12.07        12.43        12.30        11.31        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4441 
       11.77        12.62         3.02        27.02         8.05        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 
       21.07        20.55        18.84        18.61        13.35        15.22 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.79        24.72        16.80        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET 
       20.91        16.44         5.92        36.43        13.78        26.43 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.31        11.44        20.32         4.34        19.96         7.13 
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-A9TM TCGA-HF-7132 
       17.06        59.54         5.03        13.58         6.21        77.29 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       63.06        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 
       22.32        21.07         0.76        24.30         5.59        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       20.25         2.10        12.95        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       36.36         3.45        18.81        12.46        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93J 
       12.59        10.62        15.75        13.51        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13        16.67        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87        19.04         0.92        18.48        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        1.87         9.27        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91W TCGA-VQ-A91Y 
       39.45        11.70        21.83        18.74        60.85         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA64 
        2.01        55.43         6.58         5.72         2.66        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       28.41        38.93        54.12        16.14        17.26         0.79 

  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE 
                          0.26                           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 
                        13.870                         14.025 
[1] "0.3 - 122.3 (13.9)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1.1"
D29V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(13Q22.1) MUTATED         5        6       16       15        27
  AMP PEAK 29(13Q22.1) WILD-TYPE       5       15       31       18        60
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(13Q22.1) MUTATED          37         9         38         27
  AMP PEAK 29(13Q22.1) WILD-TYPE        50        19         57         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 29(13Q22.1) MUTATED           15       22         2
  AMP PEAK 29(13Q22.1) WILD-TYPE         31       27         2
D29V3, multiclass
            clus
vv           AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                              6                             15
  STAGE IB                             16                             31
  STAGE II                             15                             18
  STAGE IIA                            27                             60
  STAGE IIB                            37                             50
  STAGE III                             9                             19
  STAGE IIIA                           38                             57
  STAGE IIIB                           27                             45
  STAGE IIIC                           15                             31
  STAGE IV                             22                             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 29(13Q22.1) MUTATED      21  55 108  43
  AMP PEAK 29(13Q22.1) WILD-TYPE    34  81 175  81
D29V4, multiclass
       clus
vv      AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  T0+T1                           21                             34
  T2                              55                             81
  T3                             108                            175
  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    69  74  45  36
  AMP PEAK 29(13Q22.1) WILD-TYPE 138 113  53  60
D29V5, multiclass
    clus
vv   AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  N0                           69                            138
  N1                           74                            113
  N2                           45                             53
  N3                           36                             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"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED   202  15
  AMP PEAK 29(13Q22.1) WILD-TYPE 322  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED    202   15
  AMP PEAK 29(13Q22.1) WILD-TYPE  322   24
   clus
vv  AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  0                          202                            322
  1                           15                             24
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED    61 182
  AMP PEAK 29(13Q22.1) WILD-TYPE 124 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED     61  182
  AMP PEAK 29(13Q22.1) WILD-TYPE  124  258
        clus
vv       AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  FEMALE                           61                            124
  MALE                            182                            258
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED   174  43
  AMP PEAK 29(13Q22.1) WILD-TYPE 271  76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED    174   43
  AMP PEAK 29(13Q22.1) WILD-TYPE  271   76
     clus
vv    AMP PEAK 29(13Q22.1) MUTATED AMP PEAK 29(13Q22.1) WILD-TYPE
  NO                           174                            271
  YES                           43                             76
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(13Q22.1) MUTATED      49                         9
  AMP PEAK 29(13Q22.1) WILD-TYPE    85                         8
                                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     146
  AMP PEAK 29(13Q22.1) WILD-TYPE   246
D29V11, multiclass
                                           clus
vv                                          AMP PEAK 29(13Q22.1) MUTATED
  ASIAN                                                               49
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              146
                                           clus
vv                                          AMP PEAK 29(13Q22.1) WILD-TYPE
  ASIAN                                                                 85
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                                cls
clus                               0   1
  AMP PEAK 29(13Q22.1) MUTATED     7 151
  AMP PEAK 29(13Q22.1) WILD-TYPE   4 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(13Q22.1) MUTATED      7  151
  AMP PEAK 29(13Q22.1) WILD-TYPE    4  253
                        clus
vv                       AMP PEAK 29(13Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          151
                        clus
vv                       AMP PEAK 29(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            253
[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    59  49
  AMP PEAK 30(14Q13.3) WILD-TYPE 295 196
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                           108                            491 
  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                            49                            196 
$`AMP PEAK 30(14Q13.3) MUTATED`
TCGA-L5-A43J TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-2H-A9GF 
        4.31        35.97        20.02        47.05        21.99        25.78 
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A50L 
        5.92        32.45         0.85        20.78        18.64         0.53 
TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E 
        9.96        12.16        47.38        23.18         3.16        30.25 
TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-LN-A49K 
        3.16         7.43         5.49        21.37        13.41         5.92 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A1 
       10.45        13.41        13.15        15.35        12.59        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HX 
       12.59        22.39        11.54        13.22        12.33        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.03        13.18        12.33         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-S8-A6BW TCGA-V5-AASX 
       12.26         8.02        38.40        53.95        20.38         8.98 
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-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        25.08        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-BR-4187 TCGA-BR-6705 TCGA-BR-7717 
        1.32        19.73        58.03         4.64        25.61        18.15 
TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8486 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
       11.44         2.20        20.22        13.51        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5804 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-5732 TCGA-D7-5579 
       21.44        12.10        12.43         7.99        69.04        20.91 
TCGA-D7-6518 TCGA-D7-6818 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-HU-8243 TCGA-HU-8249 
       19.13        12.36        15.65         0.62         5.92        28.96 
TCGA-HU-A4GC TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
        3.25        18.81        18.38         6.74         6.51        10.62 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-VQ-A8E0 
       45.67        18.21         8.52        11.05        35.61        18.48 
TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V 
       22.19        17.85        14.33        18.74         1.71        42.64 
TCGA-VQ-A925 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-ZQ-A9CR 
        4.54        42.54        43.66        17.13        16.14         0.79 

$`AMP PEAK 30(14Q13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       22.98        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.35        26.93        31.27        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D 
       35.21         2.63        20.12         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-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        68.02         3.68        41.52        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF 
       31.56        25.22        24.03         6.28         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        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        15.48 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        2.60        25.12         7.40         3.75         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-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        7.76         8.71        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W 
       10.36        12.66        12.43        12.33        13.38        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.62        12.46        12.49        12.76        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8I0 
       12.33         4.47        25.25        10.52        12.00        13.38 
TCGA-LN-A8I1 TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       13.18        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04         6.35         9.30        15.78         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
       12.69         7.00         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU 
        9.27        25.81        27.09        22.82         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-AAPN 
       33.70        52.27        18.05        18.21        41.23         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-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-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        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39        25.18         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        28.34         0.66        32.52         0.46 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.65        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        13.35        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        7.17        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       15.39        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-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-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        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-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19        18.21        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
       22.29         8.38         4.34        19.96         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 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-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        18.15        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        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         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        12.46        13.35        19.53         6.44        12.59 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI 
       37.64        36.95         3.72        19.73        14.04        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        6.08         4.60         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-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        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-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-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       73.41        39.45        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       32.88        60.85         9.50         9.73        55.56         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        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        2.66        11.24        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        27.55        12.43        17.26 

  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE 
                          0.13                           0.00 
  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                          14.07 
[1] "0.1 - 69.0 (13.2)"  "0.0 - 122.3 (14.1)"
[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        22
  AMP PEAK 30(14Q13.3) WILD-TYPE       8       18       42       32        65
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(14Q13.3) MUTATED          16         8         19         10
  AMP PEAK 30(14Q13.3) WILD-TYPE        71        20         76         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 30(14Q13.3) MUTATED            7        9         1
  AMP PEAK 30(14Q13.3) WILD-TYPE         39       40         3
D30V3, multiclass
            clus
vv           AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  STAGE I                               2                              8
  STAGE IA                              3                             18
  STAGE IB                              5                             42
  STAGE II                              1                             32
  STAGE IIA                            22                             65
  STAGE IIB                            16                             71
  STAGE III                             8                             20
  STAGE IIIA                           19                             76
  STAGE IIIB                           10                             62
  STAGE IIIC                            7                             39
  STAGE IV                              9                             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 30(14Q13.3) MUTATED       8  31  49  18
  AMP PEAK 30(14Q13.3) WILD-TYPE    47 105 234 106
D30V4, multiclass
       clus
vv      AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  T0+T1                            8                             47
  T2                              31                            105
  T3                              49                            234
  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    39  34  14  19
  AMP PEAK 30(14Q13.3) WILD-TYPE 168 153  84  77
D30V5, multiclass
    clus
vv   AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  N0                           39                            168
  N1                           34                            153
  N2                           14                             84
  N3                           19                             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"
D30V6, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED    94   7
  AMP PEAK 30(14Q13.3) WILD-TYPE 430  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED     94    7
  AMP PEAK 30(14Q13.3) WILD-TYPE  430   32
   clus
vv  AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  0                           94                            430
  1                            7                             32
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED    22  91
  AMP PEAK 30(14Q13.3) WILD-TYPE 163 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED     22   91
  AMP PEAK 30(14Q13.3) WILD-TYPE  163  349
        clus
vv       AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  FEMALE                           22                            163
  MALE                             91                            349
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED    75  31
  AMP PEAK 30(14Q13.3) WILD-TYPE 370  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED     75   31
  AMP PEAK 30(14Q13.3) WILD-TYPE  370   88
     clus
vv    AMP PEAK 30(14Q13.3) MUTATED AMP PEAK 30(14Q13.3) WILD-TYPE
  NO                            75                            370
  YES                           31                             88
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(14Q13.3) MUTATED      31                         4
  AMP PEAK 30(14Q13.3) WILD-TYPE   103                        13
                                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      65
  AMP PEAK 30(14Q13.3) WILD-TYPE   327
D30V11, multiclass
                                           clus
vv                                          AMP PEAK 30(14Q13.3) MUTATED
  ASIAN                                                               31
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               65
                                           clus
vv                                          AMP PEAK 30(14Q13.3) WILD-TYPE
  ASIAN                                                                103
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                327
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK 30(14Q13.3) MUTATED     4  71
  AMP PEAK 30(14Q13.3) WILD-TYPE   7 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(14Q13.3) MUTATED      4   71
  AMP PEAK 30(14Q13.3) WILD-TYPE    7  333
                        clus
vv                       AMP PEAK 30(14Q13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       AMP PEAK 30(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            333
[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    89  72
  AMP PEAK 31(15Q26.1) WILD-TYPE 265 173
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                           161                            438 
  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                            72                            173 
$`AMP PEAK 31(15Q26.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A88Y TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-VQ-A8PU 
       60.39         0.36        47.05        22.98        79.07        27.35 
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-A6FE TCGA-L5-A43C TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR 
        3.68         3.16        47.93         7.17         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        15.48         2.60 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NJ TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NW 
        3.75        55.50        16.47        21.37        13.41        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A5 TCGA-LN-A4MR 
       10.85        10.36        10.45        13.38        22.39        13.22 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       10.52        12.00        12.23        12.33        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        7.59        16.31         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        27.09        22.82         1.55        18.31 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-ZR-A9CJ TCGA-BR-4183 
       11.24         9.17        25.08        41.23        19.73         6.61 
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 
       18.35         6.18        19.33        12.16         9.21        33.63 
TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8361 TCGA-BR-8364 
       18.15        33.21        11.44         0.69        31.10        22.19 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4PF 
        9.86         8.22         7.53        34.98         0.53         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       21.44        13.02        13.15        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-4449 
       12.30        15.39        12.07         6.31         6.58        19.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       30.97         6.97         1.02        12.03         4.01        69.04 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       20.91        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 
       12.36        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-FP-A9TM TCGA-HF-7133 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH 
        0.56         6.21        63.06        22.68        25.81        11.77 
TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        0.26        23.80        33.40         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 
       18.38        19.53         5.56        63.62        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV 
       45.67        18.21         6.08         9.24         8.61       122.30 
TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        8.94         0.92        13.02        18.48        37.22         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91K 
       46.26        22.19        12.79         2.70        17.85        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T 
       20.81         9.50         9.04         4.54        66.81        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       18.41        43.66        32.94        17.13        54.12 

$`AMP PEAK 31(15Q26.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        34.85        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       20.02        21.99        16.24         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM 
       26.93        25.78        31.27        14.30         5.92        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24         4.21         7.69        33.27        35.21         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-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-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
       18.35         3.32         7.43        25.12         7.40         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM 
        2.66        12.92        13.48        13.55        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M 
        5.49         8.71        83.24        52.57         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.25        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        12.85        15.52        11.54        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.33        25.25        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ 
        0.13        12.03        12.85        12.26         8.02         5.06 
TCGA-R6-A6XG TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       38.40         2.89         2.30        12.69         7.00         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       12.43         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD 
       46.19        18.05        15.91        18.21        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32         2.66        58.03        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-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90        36.16        35.24        35.84        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       15.32        28.73         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        13.08         0.26        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       20.88        10.68        34.13        13.87         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       20.42        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.10        12.76        12.53        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       11.64        12.82        12.43        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61        12.20        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       18.97         7.07        12.00        36.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        12.66        19.13        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       17.85        17.19        10.26        12.79        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
       19.96         7.13         7.99        14.47        21.27         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-7132 
       14.07        22.29        59.54         5.03         5.52        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        24.26        24.20         3.25        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         2.10        12.95        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
       14.07        15.68        36.36        12.46        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       13.51         2.53        36.95         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       74.53         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 
       43.36        21.73        37.41        38.14        30.97        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        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       11.70        21.83        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85         9.73        55.56         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        38.93 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE 
                          0.26                           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 
                        13.580                         14.025 
[1] "0.3 - 122.3 (13.6)" "0.0 - 116.4 (14.0)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 31(15Q26.1) MUTATED         5        6       11        9        25
  AMP PEAK 31(15Q26.1) WILD-TYPE       5       15       36       24        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 31(15Q26.1) MUTATED          16         8         28         17
  AMP PEAK 31(15Q26.1) WILD-TYPE        71        20         67         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 31(15Q26.1) MUTATED            8       18         1
  AMP PEAK 31(15Q26.1) WILD-TYPE         38       31         3
D31V3, multiclass
            clus
vv           AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                              6                             15
  STAGE IB                             11                             36
  STAGE II                              9                             24
  STAGE IIA                            25                             62
  STAGE IIB                            16                             71
  STAGE III                             8                             20
  STAGE IIIA                           28                             67
  STAGE IIIB                           17                             55
  STAGE IIIC                            8                             38
  STAGE IV                             18                             31
  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      15  44  74  25
  AMP PEAK 31(15Q26.1) WILD-TYPE    40  92 209  99
D31V4, multiclass
       clus
vv      AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  T0+T1                           15                             40
  T2                              44                             92
  T3                              74                            209
  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    52  50  33  21
  AMP PEAK 31(15Q26.1) WILD-TYPE 155 137  65  75
D31V5, multiclass
    clus
vv   AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  N0                           52                            155
  N1                           50                            137
  N2                           33                             65
  N3                           21                             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   130  14
  AMP PEAK 31(15Q26.1) WILD-TYPE 394  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED    130   14
  AMP PEAK 31(15Q26.1) WILD-TYPE  394   25
   clus
vv  AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  0                          130                            394
  1                           14                             25
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED    41 127
  AMP PEAK 31(15Q26.1) WILD-TYPE 144 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED     41  127
  AMP PEAK 31(15Q26.1) WILD-TYPE  144  313
        clus
vv       AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  FEMALE                           41                            144
  MALE                            127                            313
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED   114  38
  AMP PEAK 31(15Q26.1) WILD-TYPE 331  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED    114   38
  AMP PEAK 31(15Q26.1) WILD-TYPE  331   81
     clus
vv    AMP PEAK 31(15Q26.1) MUTATED AMP PEAK 31(15Q26.1) WILD-TYPE
  NO                           114                            331
  YES                           38                             81
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(15Q26.1) MUTATED      31                         7
  AMP PEAK 31(15Q26.1) WILD-TYPE   103                        10
                                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     102
  AMP PEAK 31(15Q26.1) WILD-TYPE   290
D31V11, multiclass
                                           clus
vv                                          AMP PEAK 31(15Q26.1) MUTATED
  ASIAN                                                               31
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              102
                                           clus
vv                                          AMP PEAK 31(15Q26.1) WILD-TYPE
  ASIAN                                                                103
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                290
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK 31(15Q26.1) MUTATED     4  93
  AMP PEAK 31(15Q26.1) WILD-TYPE   7 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(15Q26.1) MUTATED      4   93
  AMP PEAK 31(15Q26.1) WILD-TYPE    7  311
                        clus
vv                       AMP PEAK 31(15Q26.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       AMP PEAK 31(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            311
[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   125  90
  AMP PEAK 32(17Q12) WILD-TYPE 229 155
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         215                          384 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                          90                          155 
$`AMP PEAK 32(17Q12) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39        34.85        18.28        24.00        35.97        27.12 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-2H-A9GF 
       47.05        21.99        22.98        16.24         0.23        25.78 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3QL 
       14.30        58.55        13.94         8.94         7.69        35.21 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        0.53        17.03        12.82        23.18        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
       30.25         0.30        18.35         3.32         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NH 
        4.90        29.00         7.13         2.60         7.40        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-LN-A49L 
       13.48        16.47        13.22         5.49         8.71        10.45 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.38        13.15        15.35        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-M9-A5M8 
       12.59        15.52        13.18        12.33        13.18        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC 
       53.95        15.78         2.30        12.69        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET 
       16.44        15.35         9.27         8.98        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7I TCGA-X8-AAAR 
       18.31        28.11        46.19        11.24        15.91        18.21 
TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7197 
       25.08         2.10        58.03        11.70         9.17         9.21 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       33.63        18.15        33.21        14.43        11.44         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 
       29.42         2.66        15.58        14.04        14.79         5.39 
TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U 
       20.22         9.34        32.58        20.88        10.68        13.87 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4PE 
       34.98         1.48        12.89         0.72         0.53        20.42 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8529 
       21.44        13.02        13.15        12.10        12.59        12.30 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4440 
        6.31        11.31        20.02         3.02         7.99         4.01 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5722 
       19.07        12.03        18.97        30.97         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.03         4.01        69.04        18.54        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 
       10.26        15.98        12.79        11.31        12.33        19.50 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV 
       14.66        20.91        14.27        16.44        36.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 
       11.44        22.29        15.65         4.34         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8238 
       72.23         3.48        14.07         0.56        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        18.15        22.82        24.26        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        33.40        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.35        19.53         6.44         6.74        12.59        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR 
       11.70        15.75         2.53        14.04        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        37.41         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        29.59        73.41 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
       20.81        32.88        42.64         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        66.81        21.04        42.54        43.66        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        54.12        26.04        27.55         0.79 

$`AMP PEAK 32(17Q12) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-5727 TCGA-KB-A93G TCGA-MX-A663 
        0.36         5.16        20.02        79.07        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GO 
       27.35        26.93        31.27         7.63         5.92        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        4.21        32.45        33.27         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         3.88         9.30         0.79        23.41 
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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
       44.75        68.02         3.68        41.52        47.38        21.70 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         6.28         3.16        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W 
       47.93         7.17         3.16         7.43        15.48        25.12 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NK TCGA-L5-A8NM 
        3.75         3.02        55.50         2.66        13.55         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.25        12.62        12.46        12.59        22.39        12.85 
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-A8I0 TCGA-LN-A9FO 
       10.52        12.00        12.23        12.03        13.38         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.03        12.85        12.26        16.31         6.35         9.30 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        2.89         7.00         5.29        25.81        27.09        22.82 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
        8.12        33.70        18.18        52.27        18.05         9.17 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       41.23        14.37         3.42         1.32         2.66        19.73 
TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       26.70        19.56        11.01         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-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        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
       21.90        36.16        35.24        35.84        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 
       28.73         3.45         9.07        29.56        37.25        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         8.05         0.56        19.96         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
       31.27         7.36        25.05         3.72        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79        27.12        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T 
       26.73        24.79        31.96         9.86         8.22        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        7.53         6.08        27.55        28.57         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
        1.15        16.14         5.13        13.41        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       11.21        12.76        12.53         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
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-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       15.22        12.36        24.72        16.80        17.19        18.21 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       21.14         5.92        13.78        14.76        26.43        11.31 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         8.38        19.96         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       11.38        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       13.58         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       30.51        24.39        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ 
       24.30         5.59        22.68        24.20         3.25        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NR 
       15.68        36.36         3.45         3.39        12.46         6.51 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         5.56        63.62        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
       19.73        45.67         8.52        74.53         4.60        11.05 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        5.13        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
      116.38        71.38        57.44        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79        48.79        43.36        21.73        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP 
       30.97        34.29        16.31         2.50         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        13.35        64.57        14.33        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       21.83        61.22        18.74         1.71        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T 
       55.56        55.43         6.58         5.72         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       18.41        28.41        38.93        16.14        12.43        17.26 

  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                        0.23                         0.00 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                       73.41                       122.30 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                       13.35                        14.35 
[1] "0.2 - 73.4 (13.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D32V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 32(17Q12) MUTATED         4        7       16        8        28
  AMP PEAK 32(17Q12) WILD-TYPE       6       14       31       25        59
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 32(17Q12) MUTATED          26        18         29         27
  AMP PEAK 32(17Q12) WILD-TYPE        61        10         66         45
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 32(17Q12) MUTATED           13       25         2
  AMP PEAK 32(17Q12) WILD-TYPE         33       24         2
D32V3, multiclass
            clus
vv           AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  STAGE I                             4                            6
  STAGE IA                            7                           14
  STAGE IB                           16                           31
  STAGE II                            8                           25
  STAGE IIA                          28                           59
  STAGE IIB                          26                           61
  STAGE III                          18                           10
  STAGE IIIA                         29                           66
  STAGE IIIB                         27                           45
  STAGE IIIC                         13                           33
  STAGE IV                           25                           24
  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  48  96  42
  AMP PEAK 32(17Q12) WILD-TYPE    32  88 187  82
D32V4, multiclass
       clus
vv      AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  T0+T1                         23                           32
  T2                            48                           88
  T3                            96                          187
  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    67  67  37  35
  AMP PEAK 32(17Q12) WILD-TYPE 140 120  61  61
D32V5, multiclass
    clus
vv   AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  N0                         67                          140
  N1                         67                          120
  N2                         37                           61
  N3                         35                           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   169  21
  AMP PEAK 32(17Q12) WILD-TYPE 355  18
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED    169   21
  AMP PEAK 32(17Q12) WILD-TYPE  355   18
   clus
vv  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  0                        169                          355
  1                         21                           18
[1] 2 2
[1] FALSE
D32V7, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED    50 172
  AMP PEAK 32(17Q12) WILD-TYPE 135 268
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED     50  172
  AMP PEAK 32(17Q12) WILD-TYPE  135  268
        clus
vv       AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  FEMALE                         50                          135
  MALE                          172                          268
[1] 2 2
[1] FALSE
D32V8, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED   147  47
  AMP PEAK 32(17Q12) WILD-TYPE 298  72
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED    147   47
  AMP PEAK 32(17Q12) WILD-TYPE  298   72
     clus
vv    AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  NO                         147                          298
  YES                         47                           72
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(17Q12) MUTATED      40                        11
  AMP PEAK 32(17Q12) WILD-TYPE    94                         6
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 32(17Q12) MUTATED                                           1   137
  AMP PEAK 32(17Q12) WILD-TYPE                                         0   255
D32V11, multiclass
                                           clus
vv                                          AMP PEAK 32(17Q12) MUTATED
  ASIAN                                                             40
  BLACK OR AFRICAN AMERICAN                                         11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            137
                                           clus
vv                                          AMP PEAK 32(17Q12) WILD-TYPE
  ASIAN                                                               94
  BLACK OR AFRICAN AMERICAN                                            6
  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"
D32V12, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED     3 131
  AMP PEAK 32(17Q12) WILD-TYPE   8 273
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED      3  131
  AMP PEAK 32(17Q12) WILD-TYPE    8  273
                        clus
vv                       AMP PEAK 32(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        131
                        clus
vv                       AMP PEAK 32(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          273
[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   106  65
  AMP PEAK 33(18P11.32) WILD-TYPE 248 180
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                            171                             428 
  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                             65                             180 
$`AMP PEAK 33(18P11.32) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-L5-A8NT 
       60.39        34.85         4.31         8.94         0.36        27.12 
TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-VQ-A94U TCGA-2H-A9GK TCGA-2H-A9GM 
       21.99        22.98         0.23        26.93         7.63        13.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A50L TCGA-IG-A625 TCGA-IG-A97H 
       16.24         4.21        32.45         0.53        12.82        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE TCGA-L5-A43C TCGA-L5-A4OM TCGA-L5-A4OO 
       12.16        44.75         3.68         3.16        47.93         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A8NF 
        1.38         3.16         4.90         7.13         2.60         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW 
       13.48        16.47        13.22         5.49        21.37        46.09 
TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       10.36        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ 
       13.25        12.62        12.46        12.76        12.59        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I1 
       13.22         4.47        25.25        12.03        13.18        13.18 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW 
       12.85        12.26         5.06        53.95        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        3.42        16.44        28.11        18.18        52.27        11.24 
TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
        9.17        25.08        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6565 
        2.66         9.44         6.97        18.35         9.67         9.17 
TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
        9.21        39.78        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        26.73         8.22 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD 
       13.87        34.98        12.89         0.72        13.51        20.65 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8529 
       13.41        13.02        13.15        12.10        12.53        12.30 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-5724 TCGA-D7-6518 TCGA-D7-6520 
        6.31        12.30        12.20        12.03        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 
       18.54        17.19        10.26        15.22        12.79        14.66 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C 
       13.78        11.31        22.29        15.65        19.96        11.38 
TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 
       19.53         0.56         5.52         6.21        63.06        26.47 
TCGA-HU-8243 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU 
        5.92        21.07         0.76        22.75        25.81         6.58 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       23.84        33.40        18.38        19.53         6.44         6.74 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       10.62        15.75        63.62        14.04        45.67        18.21 
TCGA-R5-A7ZI TCGA-RD-A7BT TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8E3 
       74.53         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        21.83 
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        66.81         2.66 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       43.66        38.93         0.79 

$`AMP PEAK 33(18P11.32) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        18.28        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97         5.16        20.02        47.05        79.07        16.24 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        27.35        25.78        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL 
       58.55         5.92         8.94         7.69        33.27        35.21 
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-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP 
        9.30        17.03         0.79        23.41         9.96        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
        4.67       122.10        68.02        41.52        47.38        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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        26.33        32.61        21.01        18.35         7.17 
TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
       58.59        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM 
        3.75         3.02        55.50        12.92        13.55         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
        8.71        13.41        83.24        52.57        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A2 
       10.45        12.66        12.43        13.38        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HV 
       22.39        12.85        15.52        11.54        12.33        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.33        13.38         0.13        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
       38.40         6.35         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        7.00         5.29        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       27.09        22.82        12.43         1.55        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       33.70        46.19        18.05        15.91        18.21        41.23 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        9.47         6.61         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 
       36.16        35.24        35.84        33.63        18.15        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        9.07        29.56        33.21        37.25        14.43        29.59 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 
       32.25         0.56        29.42         2.66        19.96         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 
       25.05         3.72         5.39        25.18        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 
       32.58         9.86        20.88        10.68        34.13         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34         0.66        32.52         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 
        1.15        21.44        16.14         5.13        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       11.21        12.76        12.59         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.31        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 
       20.55        18.61        17.85        13.35        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27         3.48        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
       59.54         5.03        13.58        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
        3.39        12.46        13.35        12.59         6.51        11.70 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG 
       13.51         2.53         5.56        37.64        36.95         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73         8.52         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-A8N2 
        5.13        16.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       71.38        57.44         8.94        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
       48.79         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         2.50        12.79        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       11.70        61.22        20.81        32.88        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        55.56         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        5.72        21.04        42.54        11.24        18.41        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE 
                           0.23                            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 
                         12.820                          15.585 
[1] "0.2 - 115.7 (12.8)" "0.0 - 122.3 (15.6)"
[1] "hr=" "1.1"
D33V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 33(18P11.32) MUTATED         2        6       10        6        26
  AMP PEAK 33(18P11.32) WILD-TYPE       8       15       37       27        61
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 33(18P11.32) MUTATED          28        13         21         14
  AMP PEAK 33(18P11.32) WILD-TYPE        59        15         74         58
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 33(18P11.32) MUTATED           18       15         3
  AMP PEAK 33(18P11.32) WILD-TYPE         28       34         1
D33V3, multiclass
            clus
vv           AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  STAGE I                                2                               8
  STAGE IA                               6                              15
  STAGE IB                              10                              37
  STAGE II                               6                              27
  STAGE IIA                             26                              61
  STAGE IIB                             28                              59
  STAGE III                             13                              15
  STAGE IIIA                            21                              74
  STAGE IIIB                            14                              58
  STAGE IIIC                            18                              28
  STAGE IV                              15                              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 33(18P11.32) MUTATED      18  30  86  34
  AMP PEAK 33(18P11.32) WILD-TYPE    37 106 197  90
D33V4, multiclass
       clus
vv      AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  T0+T1                            18                              37
  T2                               30                             106
  T3                               86                             197
  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    56  56  22  32
  AMP PEAK 33(18P11.32) WILD-TYPE 151 131  76  64
D33V5, multiclass
    clus
vv   AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  N0                            56                             151
  N1                            56                             131
  N2                            22                              76
  N3                            32                              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   143  13
  AMP PEAK 33(18P11.32) WILD-TYPE 381  26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED    143   13
  AMP PEAK 33(18P11.32) WILD-TYPE  381   26
   clus
vv  AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  0                           143                             381
  1                            13                              26
[1] 2 2
[1] FALSE
D33V7, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED    46 132
  AMP PEAK 33(18P11.32) WILD-TYPE 139 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED     46  132
  AMP PEAK 33(18P11.32) WILD-TYPE  139  308
        clus
vv       AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  FEMALE                            46                             139
  MALE                             132                             308
[1] 2 2
[1] FALSE
D33V8, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED   125  37
  AMP PEAK 33(18P11.32) WILD-TYPE 320  82
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED    125   37
  AMP PEAK 33(18P11.32) WILD-TYPE  320   82
     clus
vv    AMP PEAK 33(18P11.32) MUTATED AMP PEAK 33(18P11.32) WILD-TYPE
  NO                            125                             320
  YES                            37                              82
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(18P11.32) MUTATED      46                         3
  AMP PEAK 33(18P11.32) WILD-TYPE    88                        14
                                 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     108
  AMP PEAK 33(18P11.32) WILD-TYPE   284
D33V11, multiclass
                                           clus
vv                                          AMP PEAK 33(18P11.32) MUTATED
  ASIAN                                                                46
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               108
                                           clus
vv                                          AMP PEAK 33(18P11.32) WILD-TYPE
  ASIAN                                                                  88
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 284
[1] 4 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, binary
                                 cls
clus                                0   1
  AMP PEAK 33(18P11.32) MUTATED     5 114
  AMP PEAK 33(18P11.32) WILD-TYPE   6 290
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(18P11.32) MUTATED      5  114
  AMP PEAK 33(18P11.32) WILD-TYPE    6  290
                        clus
vv                       AMP PEAK 33(18P11.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           114
                        clus
vv                       AMP PEAK 33(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             290
[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   112  76
  AMP PEAK 34(18Q11.2) WILD-TYPE 242 169
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                           188                            411 
  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                            76                            169 
$`AMP PEAK 34(18Q11.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-CG-4460 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GJ 
       27.12        21.99         0.23         9.86        26.93        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A50L TCGA-IG-A625 
        7.63        13.94         4.21        33.27         0.53        12.82 
TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR 
       47.38         3.16        30.25        18.35         3.32         3.16 
TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI 
        7.13         2.60         3.02        55.50         2.66        13.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         5.49        13.41        83.24        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4MQ 
       10.36         5.92        12.62        12.76        12.59        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DQ 
       25.25        13.18        13.18        12.26         7.82         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
        5.06        38.40        53.95        15.78        12.69        20.38 
TCGA-V5-A7RE TCGA-VR-A8EQ TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I 
       16.44        22.82        18.18        52.27        11.24        15.91 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-A5TN TCGA-BR-4184 
        2.10         1.32         2.66        58.03         9.44         6.97 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-7715 
        7.43        18.35         9.67        26.10         9.17        33.63 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
       15.32        28.73         3.45         0.69         9.60         8.05 
TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8370 
       29.42         2.20        15.58         7.40        13.08         3.32 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
       14.79         3.72        25.18        20.22         1.12        27.12 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ 
       26.73        24.79        20.88         8.22        13.87        34.98 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF 
       12.89         0.72         0.66        13.51        20.65         1.15 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8529 
       13.41        13.02        13.15        12.10        12.53        12.30 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4440 
        6.31        12.43        12.20        20.02         3.02         4.01 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5724 TCGA-D7-5579 
       14.01        19.07         7.07        12.00        12.03        20.91 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       19.13        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       12.79        14.66        13.78        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8631 
       22.29        19.96         0.62        72.23        11.38         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8245 
        5.52         6.21        63.06        26.47         5.92        18.15 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.76        22.75         8.98        23.84        23.80        21.17 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       33.40        18.81        18.38        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 
        6.74        11.70        15.75        63.62        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A805 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N1 
       45.67        74.53         9.24         5.13        16.67       115.69 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       35.61         5.79         0.92         5.46        13.02        18.48 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91N 
        2.70         1.87         9.27        73.41        21.83        18.74 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA68 
        1.71        42.64         9.04        66.81        42.54        43.66 
TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       38.93         0.79 

$`AMP PEAK 34(18Q11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        47.05        22.98        79.07        16.24 
TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
       20.15        27.35        25.78        31.27        14.30         5.92 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 
        8.94        16.24        32.45         7.69        35.21         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-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 
       17.03         0.79        23.41         9.96        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.50        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        6.28         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX 
        7.17         1.38        58.59         4.90        29.00         7.43 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NJ 
       15.48        25.12         7.40         3.75        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L7-A56G TCGA-LN-A49L 
       13.55         7.76        21.37         8.71        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        12.59        13.25        12.46        12.59        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ 
       12.33        10.52        12.00        12.23        12.03        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-R6-A6DN 
       13.38         0.13        12.03        12.85        33.11         8.02 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
       16.31         7.04         6.35         9.30         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        7.00         5.29         3.42        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       25.81        27.09        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        33.70        46.19        18.05         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 
       25.08        41.23        14.37         3.42        19.73        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 
       11.70        19.56        11.01         9.47         6.61         4.64 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-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        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       18.15         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       11.44        29.59        32.25         0.56         2.66        19.96 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        31.10         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
       26.33         4.31        14.04        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       25.05         5.39         9.21        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        6.28         7.53        31.96        32.58         9.86        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17         0.53        28.34        32.52         0.46 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 
       20.42        21.44        16.14         5.13        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       11.21        12.76        12.59         7.17        12.33        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        11.31        11.61         6.58        11.77        12.62 
TCGA-CG-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-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 
       29.98        12.03         0.00         9.01        18.97        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       18.61        17.85        15.98        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       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        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        20.32        15.65         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.99        14.47        21.27         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 
       22.29        17.06        59.54         5.03        13.58        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       52.21        30.51         1.51        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        29.00        14.07        15.68        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
        3.39        12.46        12.59         6.51        10.62        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        2.53         5.56        36.95         3.72        19.73        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV 
        8.52         6.08         4.60        11.05         8.61       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       16.87        19.04        48.79        13.25        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK 
       46.26        16.31        22.19         2.50        12.79        17.85 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        13.35        29.59        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W 
       39.45        11.70        61.22        20.81        32.88        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73        55.56         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58         5.72        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE 
                          0.23                           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 
                         13.18                          14.50 
[1] "0.2 - 115.7 (13.2)" "0.0 - 122.3 (14.5)"
[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       14        8        23
  AMP PEAK 34(18Q11.2) WILD-TYPE       4       15       33       25        64
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 34(18Q11.2) MUTATED          22        11         32         20
  AMP PEAK 34(18Q11.2) WILD-TYPE        65        17         63         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 34(18Q11.2) MUTATED           17       18         2
  AMP PEAK 34(18Q11.2) WILD-TYPE         29       31         2
D34V3, multiclass
            clus
vv           AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  STAGE I                               6                              4
  STAGE IA                              6                             15
  STAGE IB                             14                             33
  STAGE II                              8                             25
  STAGE IIA                            23                             64
  STAGE IIB                            22                             65
  STAGE III                            11                             17
  STAGE IIIA                           32                             63
  STAGE IIIB                           20                             52
  STAGE IIIC                           17                             29
  STAGE IV                             18                             31
  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      20  37  86  43
  AMP PEAK 34(18Q11.2) WILD-TYPE    35  99 197  81
D34V4, multiclass
       clus
vv      AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  T0+T1                           20                             35
  T2                              37                             99
  T3                              86                            197
  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    61  58  33  34
  AMP PEAK 34(18Q11.2) WILD-TYPE 146 129  65  62
D34V5, multiclass
    clus
vv   AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  N0                           61                            146
  N1                           58                            129
  N2                           33                             65
  N3                           34                             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   160  14
  AMP PEAK 34(18Q11.2) WILD-TYPE 364  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED    160   14
  AMP PEAK 34(18Q11.2) WILD-TYPE  364   25
   clus
vv  AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  0                          160                            364
  1                           14                             25
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED    58 140
  AMP PEAK 34(18Q11.2) WILD-TYPE 127 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED     58  140
  AMP PEAK 34(18Q11.2) WILD-TYPE  127  300
        clus
vv       AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  FEMALE                           58                            127
  MALE                            140                            300
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED   137  36
  AMP PEAK 34(18Q11.2) WILD-TYPE 308  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED    137   36
  AMP PEAK 34(18Q11.2) WILD-TYPE  308   83
     clus
vv    AMP PEAK 34(18Q11.2) MUTATED AMP PEAK 34(18Q11.2) WILD-TYPE
  NO                           137                            308
  YES                           36                             83
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(18Q11.2) MUTATED      37                         3
  AMP PEAK 34(18Q11.2) WILD-TYPE    97                        14
                                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     133
  AMP PEAK 34(18Q11.2) WILD-TYPE   259
D34V11, multiclass
                                           clus
vv                                          AMP PEAK 34(18Q11.2) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              133
                                           clus
vv                                          AMP PEAK 34(18Q11.2) WILD-TYPE
  ASIAN                                                                 97
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                259
[1] 4 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, binary
                                cls
clus                               0   1
  AMP PEAK 34(18Q11.2) MUTATED     4 126
  AMP PEAK 34(18Q11.2) WILD-TYPE   7 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(18Q11.2) MUTATED      4  126
  AMP PEAK 34(18Q11.2) WILD-TYPE    7  278
                        clus
vv                       AMP PEAK 34(18Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK 34(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            278
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(19Q12) MUTATION ANALYSIS
D35V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 35(19Q12) MUTATED   104  70
  AMP PEAK 35(19Q12) WILD-TYPE 250 175
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                         174                          425 
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                          70                          175 
$`AMP PEAK 35(19Q12) MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       24.00        35.97        27.12        47.05        21.99        22.98 
TCGA-EQ-A4SO TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-IC-A6RE 
       16.24        31.27        58.55         7.63         8.94         7.69 
TCGA-IG-A3QL TCGA-IG-A4QS TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FH TCGA-L5-A43C 
       35.21         3.88        23.41        14.50        47.38         3.16 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       26.33        32.61        18.35         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR 
       58.59         3.75        55.50        13.55         5.49         8.71 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A7HW 
       12.33        15.35        12.59        22.39        12.85        12.00 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG 
        0.13        12.85        12.26         5.06        16.31        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-AASV TCGA-VR-A8EX 
       53.95        15.78        12.69        20.38        15.35        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-B7-A5TK 
       52.27        15.91        18.21        25.08         2.10         9.47 
TCGA-BR-4253 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 
        4.08        17.29        19.33         9.21        33.63        39.78 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 
       28.73         3.45        33.21        11.44         0.69        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8485 
        2.66        19.96         2.20         3.32        14.79         9.21 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 
        1.12         9.34        24.79        10.68         6.08         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.51        20.65        21.44        13.15        13.18        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
       12.76        12.59        12.53        12.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4449 
       12.30        12.43        11.61        12.20        54.08        19.07 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        0.99         4.01        25.71        20.91        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 
       18.54        17.19        10.26        15.22        12.36        12.33 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-D7-A74B TCGA-EQ-5647 
       21.14        16.44        13.78        22.29         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BF 
        7.99        72.23         3.48        14.07         0.56         5.52 
TCGA-HF-7133 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 
       63.06        24.39        18.15        28.96        22.82        24.30 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
       22.75        25.81        11.77         2.10        12.95        23.80 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F5 
       33.40         3.45        18.38        13.35         6.44         5.56 
TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT 
       63.62        14.04        45.67        18.21         6.08         8.61 
TCGA-RD-A7BW TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        5.13        35.61         5.79        48.79         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91A 
       43.36         7.73        22.19        17.85         1.87        39.45 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 
       18.74        32.88         1.71        42.64         9.50         9.04 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6K 
        2.01         4.54        21.04        17.13        54.12        12.43 

$`AMP PEAK 35(19Q12) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV 
        4.70        19.99        22.82         0.36         5.16        20.02 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07         0.23        20.15         9.86        27.35        26.93 
TCGA-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-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45        33.27         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-A625 
       18.64         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-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-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ 
       25.22        24.03         6.28        30.25         0.30        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
       47.93         7.17         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       15.48         2.60        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.22         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
       13.41        83.24        12.66        12.43        13.41        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.49        12.76        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-A7HY 
        4.47        12.33        25.25        10.52        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       13.18        12.33        13.38        13.18        12.03        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-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.89         2.30         7.00         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        9.27         8.98        25.81        27.09        22.82        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        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05        11.24         9.17        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       19.56        11.01         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       18.15        15.32         9.07        29.56        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
       29.59         9.60        32.25         8.05         0.56        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       17.52         0.95        26.33         4.31        14.04        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22        12.79        27.12        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       26.73        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
        0.66        32.52         0.46        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8527 
        5.13        13.41        13.02        11.21        12.10         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.31         6.58        11.77        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-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-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-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       28.96        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        36.43        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        8.38         4.34        19.96        14.47        21.27        11.38 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       19.53        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
        5.92        22.32        21.07         0.76         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68        24.20         3.25        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.58        20.25         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       23.84        21.17        14.07        15.68        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        12.46        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H 
       10.62        11.70        15.75        13.51         2.53        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       36.95         3.72        19.73         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05        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-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       19.04         0.92        13.02        18.48        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.50        12.79         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       13.35        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       21.83        61.22        20.81        60.85         9.73        55.56 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       55.43         6.58         5.72        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       11.24        18.41        43.66        28.41        38.93        32.94 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        17.26         0.79 

  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                        0.13                         0.00 
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                       72.23                       122.30 
  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE 
                      13.665                       14.010 
[1] "0.1 - 72.2 (13.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D35V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 35(19Q12) MUTATED         3        5       13       10        24
  AMP PEAK 35(19Q12) WILD-TYPE       7       16       34       23        63
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 35(19Q12) MUTATED          27         8         34         19
  AMP PEAK 35(19Q12) WILD-TYPE        60        20         61         53
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 35(19Q12) MUTATED           10       14         2
  AMP PEAK 35(19Q12) WILD-TYPE         36       35         2
D35V3, multiclass
            clus
vv           AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  STAGE I                             3                            7
  STAGE IA                            5                           16
  STAGE IB                           13                           34
  STAGE II                           10                           23
  STAGE IIA                          24                           63
  STAGE IIB                          27                           60
  STAGE III                           8                           20
  STAGE IIIA                         34                           61
  STAGE IIIB                         19                           53
  STAGE IIIC                         10                           36
  STAGE IV                           14                           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 35(19Q12) MUTATED      15  40  93  27
  AMP PEAK 35(19Q12) WILD-TYPE    40  96 190  97
D35V4, multiclass
       clus
vv      AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  T0+T1                         15                           40
  T2                            40                           96
  T3                            93                          190
  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 35(19Q12) MUTATED    54  59  25  32
  AMP PEAK 35(19Q12) WILD-TYPE 153 128  73  64
D35V5, multiclass
    clus
vv   AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  N0                         54                          153
  N1                         59                          128
  N2                         25                           73
  N3                         32                           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"
D35V6, binary
                              cls
clus                             0   1
  AMP PEAK 35(19Q12) MUTATED   150  11
  AMP PEAK 35(19Q12) WILD-TYPE 374  28
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 35(19Q12) MUTATED    150   11
  AMP PEAK 35(19Q12) WILD-TYPE  374   28
   clus
vv  AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  0                        150                          374
  1                         11                           28
[1] 2 2
[1] FALSE
D35V7, binary
                              cls
clus                             0   1
  AMP PEAK 35(19Q12) MUTATED    49 136
  AMP PEAK 35(19Q12) WILD-TYPE 136 304
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 35(19Q12) MUTATED     49  136
  AMP PEAK 35(19Q12) WILD-TYPE  136  304
        clus
vv       AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  FEMALE                         49                          136
  MALE                          136                          304
[1] 2 2
[1] FALSE
D35V8, binary
                              cls
clus                             0   1
  AMP PEAK 35(19Q12) MUTATED   130  37
  AMP PEAK 35(19Q12) WILD-TYPE 315  82
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 35(19Q12) MUTATED    130   37
  AMP PEAK 35(19Q12) WILD-TYPE  315   82
     clus
vv    AMP PEAK 35(19Q12) MUTATED AMP PEAK 35(19Q12) WILD-TYPE
  NO                         130                          315
  YES                         37                           82
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 35(19Q12) MUTATED      44                         8
  AMP PEAK 35(19Q12) WILD-TYPE    90                         9
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 35(19Q12) MUTATED                                           1   108
  AMP PEAK 35(19Q12) WILD-TYPE                                         0   284
D35V11, multiclass
                                           clus
vv                                          AMP PEAK 35(19Q12) MUTATED
  ASIAN                                                             44
  BLACK OR AFRICAN AMERICAN                                          8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            108
                                           clus
vv                                          AMP PEAK 35(19Q12) WILD-TYPE
  ASIAN                                                               90
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              284
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 35(19Q12) MUTATED     3 122
  AMP PEAK 35(19Q12) WILD-TYPE   8 282
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 35(19Q12) MUTATED      3  122
  AMP PEAK 35(19Q12) WILD-TYPE    8  282
                        clus
vv                       AMP PEAK 35(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        122
                        clus
vv                       AMP PEAK 35(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          282
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 36(19Q13.43) MUTATION ANALYSIS
D36V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 36(19Q13.43) MUTATED    93  64
  AMP PEAK 36(19Q13.43) WILD-TYPE 261 181
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                            157                             442 
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                             64                             181 
$`AMP PEAK 36(19Q13.43) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-CG-4444 
       18.28         8.94        24.00         4.70        27.12        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GK 
       21.99        22.98        16.24        26.93        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4QS 
       13.94         8.94        16.24        35.21        20.12         3.88 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FE 
       23.41        12.82         4.67        14.50       122.10         3.68 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OR 
       23.18         3.16        26.33        32.61         3.32         3.16 
TCGA-L5-A88S TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       15.48        13.55         5.49        46.09        10.85        10.36 
TCGA-LN-A49K TCGA-LN-A49U TCGA-LN-A4A6 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I1 
        5.92        15.35        12.85        12.00        12.03        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.13        12.85         5.06        16.31         7.04        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
       53.95         2.89        12.69         7.00        20.38         3.42 
TCGA-V5-AASV TCGA-VR-A8EX TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-3M-AB46 
       15.35        28.11        15.91        18.21         2.10        58.03 
TCGA-B7-A5TK TCGA-BR-4253 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 
        9.47         4.08        19.33         9.21        39.78        28.73 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8295 
        3.45        29.56        33.21        29.59        29.42         2.20 
TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A453 
        3.32         9.21         1.12        24.79        10.68         6.08 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 
        0.72        13.51        20.65        13.18        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A487 TCGA-CD-A48C 
        7.17        12.39        15.39        12.07        12.30        11.61 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 
       54.08         4.01        12.00         0.99         4.01        25.71 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       19.13        18.54        17.19        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-D7-A6F0 
       24.72        21.14        16.44        13.78        20.32        22.29 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       72.23         3.48        14.07         5.52         6.21        63.06 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 
       24.30        22.75         8.98         2.10        12.95        21.17 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A6F7 
       33.40         3.45        13.35         6.44         6.74        63.62 
TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       37.64        14.04         6.08        11.05         8.61         5.13 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PE 
       35.61         5.79        48.79        13.25         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A923 
       12.79         2.70        39.45         1.71        42.64         2.01 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6I 
        5.72        66.81        21.04        42.54        11.24        16.14 
TCGA-VQ-AA6K 
       12.43 

$`AMP PEAK 36(19Q13.43) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-5727 TCGA-FP-A8CX 
        0.36        35.97         5.16        20.02        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        27.35        25.78        31.27        14.30 
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 
        5.92         4.21        32.45         7.69        33.27         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        18.64         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-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28        30.25         0.30        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         1.38        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
        7.76        21.37         8.71        13.41        83.24        52.57 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.49        12.76        12.59        22.39        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR 
       12.23        13.18        12.33        13.38        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XQ TCGA-R6-A6Y2 
       33.11         7.82         8.02         7.59         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       15.78         2.30         5.29        16.44         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G 
        8.12        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       11.24         9.17        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32         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-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       18.35        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        44.94        21.90        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 
       33.63        18.15        15.32         9.07        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69         9.60        32.25         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66        19.96        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31        14.04        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 
       25.05         3.72         5.39        25.18        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88         8.22        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52         0.46        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.10        12.59        12.33        12.30        12.59        11.64 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
       12.82        12.43         6.31        11.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.20        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         0.00         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        12.66        20.91        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.79        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27         5.92        36.43        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.31        11.44        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
       19.96         7.13         0.62         7.99        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       11.38        19.53        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
        1.51         5.92         0.76         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.58        20.25         0.26        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       23.84        23.80        14.07        15.68        36.36        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        18.38        12.46        19.53        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95         3.72        19.73        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       74.53         4.60         9.24        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       16.87        19.04         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 
       43.36        21.73        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        73.41        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81        32.88        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA64 
        9.04        55.43         4.54         6.58         2.66        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        27.55        17.26         0.79 

  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                           0.13                            0.00 
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                          122.1                           122.3 
  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE 
                          13.51                           14.12 
[1] "0.1 - 122.1 (13.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D36V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 36(19Q13.43) MUTATED         4        3       14        9        15
  AMP PEAK 36(19Q13.43) WILD-TYPE       6       18       33       24        72
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 36(19Q13.43) MUTATED          21         7         27         22
  AMP PEAK 36(19Q13.43) WILD-TYPE        66        21         68         50
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 36(19Q13.43) MUTATED            9       12         2
  AMP PEAK 36(19Q13.43) WILD-TYPE         37       37         2
D36V3, multiclass
            clus
vv           AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  STAGE I                                4                               6
  STAGE IA                               3                              18
  STAGE IB                              14                              33
  STAGE II                               9                              24
  STAGE IIA                             15                              72
  STAGE IIB                             21                              66
  STAGE III                              7                              21
  STAGE IIIA                            27                              68
  STAGE IIIB                            22                              50
  STAGE IIIC                             9                              37
  STAGE IV                              12                              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(19Q13.43) MUTATED      14  32  81  25
  AMP PEAK 36(19Q13.43) WILD-TYPE    41 104 202  99
D36V4, multiclass
       clus
vv      AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  T0+T1                            14                              41
  T2                               32                             104
  T3                               81                             202
  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 36(19Q13.43) MUTATED    48  46  23  31
  AMP PEAK 36(19Q13.43) WILD-TYPE 159 141  75  65
D36V5, multiclass
    clus
vv   AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  N0                            48                             159
  N1                            46                             141
  N2                            23                              75
  N3                            31                              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(19Q13.43) MUTATED   128  10
  AMP PEAK 36(19Q13.43) WILD-TYPE 396  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(19Q13.43) MUTATED    128   10
  AMP PEAK 36(19Q13.43) WILD-TYPE  396   29
   clus
vv  AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  0                           128                             396
  1                            10                              29
[1] 2 2
[1] FALSE
D36V7, binary
                                 cls
clus                                0   1
  AMP PEAK 36(19Q13.43) MUTATED    43 121
  AMP PEAK 36(19Q13.43) WILD-TYPE 142 319
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(19Q13.43) MUTATED     43  121
  AMP PEAK 36(19Q13.43) WILD-TYPE  142  319
        clus
vv       AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  FEMALE                            43                             142
  MALE                             121                             319
[1] 2 2
[1] FALSE
D36V8, binary
                                 cls
clus                                0   1
  AMP PEAK 36(19Q13.43) MUTATED   118  32
  AMP PEAK 36(19Q13.43) WILD-TYPE 327  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(19Q13.43) MUTATED    118   32
  AMP PEAK 36(19Q13.43) WILD-TYPE  327   87
     clus
vv    AMP PEAK 36(19Q13.43) MUTATED AMP PEAK 36(19Q13.43) WILD-TYPE
  NO                            118                             327
  YES                            32                              87
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(19Q13.43) MUTATED      40                         7
  AMP PEAK 36(19Q13.43) WILD-TYPE    94                        10
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 36(19Q13.43) MUTATED                                           1
  AMP PEAK 36(19Q13.43) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 36(19Q13.43) MUTATED      92
  AMP PEAK 36(19Q13.43) WILD-TYPE   300
D36V11, multiclass
                                           clus
vv                                          AMP PEAK 36(19Q13.43) MUTATED
  ASIAN                                                                40
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                92
                                           clus
vv                                          AMP PEAK 36(19Q13.43) WILD-TYPE
  ASIAN                                                                  94
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  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"
D36V12, binary
                                 cls
clus                                0   1
  AMP PEAK 36(19Q13.43) MUTATED     2 106
  AMP PEAK 36(19Q13.43) WILD-TYPE   9 298
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(19Q13.43) MUTATED      2  106
  AMP PEAK 36(19Q13.43) WILD-TYPE    9  298
                        clus
vv                       AMP PEAK 36(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           106
                        clus
vv                       AMP PEAK 36(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             298
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 37(20Q13.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 37(20Q13.2) MUTATED   233 171
  AMP PEAK 37(20Q13.2) WILD-TYPE 121  74
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                           404                            195 
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                           171                             74 
$`AMP PEAK 37(20Q13.2) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       35.97        27.12        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       79.07        16.24         0.23        20.15         9.86        27.35 
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-A4OF TCGA-L5-A4OH TCGA-L5-A4ON 
        3.16        30.25         0.30        26.33        32.61        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-A88V TCGA-L5-A891 
       29.00         7.13         7.43        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL 
        3.02        55.50         2.66        12.92        16.47        13.22 
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-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       10.85        10.36        10.45        12.33        13.38        13.15 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.85        12.33        25.25        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.18         0.13        12.03        12.85 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        8.02         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        7.00         5.29         3.42        16.44         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 
       27.09        22.82         1.55         8.12        28.11        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19        11.24         9.17         2.10         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       58.03        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4280 
        4.64        18.35        30.90         4.08         9.67         6.61 
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-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6852 
       26.10         9.17        18.05        19.89        40.21        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       21.90         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.32        28.73         3.45        29.56        33.21        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       11.44         0.69         9.60         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        2.20        15.58         7.40        14.04        14.79         7.36 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        24.79        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        8.22        10.68        13.87         7.53        34.98         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.89         0.72         0.53        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42         1.15        21.44        13.02        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.76        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
       12.30        12.39        11.64        15.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        12.43        11.61         6.58        12.20        11.77 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00        30.97        36.00         1.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99        12.03        15.02        28.96         4.01        69.04 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        25.71        12.66        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        36.43        26.43        11.24        11.31        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       22.29        15.65         8.38        19.96         0.62         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 
       22.29        17.06         0.56         5.52         6.21        63.06 
TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       28.96        22.82        21.07         0.76        24.30        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        15.68        33.40        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        3.39        18.38        13.35         6.74        12.59        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        13.51         2.53         5.56        63.62        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        8.61        16.67        37.91       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PE 
       13.02        18.48        43.36        21.73        46.26        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
        2.50        12.79         2.70        17.85         1.87        15.65 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N 
       64.57        14.33        73.41        39.45        21.83        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D 
       55.56         9.04         2.01         4.54         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       21.04        42.54        11.24        18.41        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        17.13        54.12        26.04        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

$`AMP PEAK 37(20Q13.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU 
       15.68        60.39        34.85        19.99        22.82         5.16 
TCGA-VQ-A94U TCGA-2H-A9GL TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
       26.93         5.92        35.21        20.78        18.64         9.30 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH 
       12.82         9.96        14.86        68.02        41.52        47.38 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A88W TCGA-L5-A88Z 
       24.03         6.28        21.01        47.93        25.12         7.40 
TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49M 
       13.48        13.55         7.76        83.24         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.43        13.41        15.35        12.46        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A8WC TCGA-S8-A6BW 
       13.38        12.26        33.11         7.82         2.30        20.38 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ 
       15.35        25.81        12.43        18.31        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       18.05        15.91        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4188 
        3.42         1.32        26.70        11.70        19.56         7.43 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 
        4.08         9.34         6.18         9.57        34.68        32.78 
TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7703 
       25.61        12.16         8.98        30.90        31.20        36.16 
TCGA-BR-7707 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       35.84         9.07        37.25        29.59        32.25         8.05 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       29.42         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 
       31.27        25.05         3.72         1.12        12.79        28.14 
TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        6.28        31.96        34.13         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
        8.98        14.17        28.34         0.66        32.52        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8534 
        5.13        13.41        13.35        11.21        12.59        12.07 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-4465 
       12.43        11.31        12.62         1.02         0.00         9.01 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
        6.97         0.99         6.02       105.07        65.10        21.07 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-A4YY 
       18.61        17.85        12.36        17.19        18.21        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-A448 TCGA-FP-8209 
       14.76        11.44         4.34         7.13        21.27        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 
        5.03        13.58        77.29        30.51        22.32         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 
       22.68        24.20        21.37        29.98         6.51        29.00 
TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR 
       14.07        18.81        12.46        19.53         6.44         6.51 
TCGA-IN-AB1V TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 
       15.75        36.95         3.72        19.73         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       16.87        19.04        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS 
       30.97        34.29        16.31         9.27        23.41        13.35 
TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 
       29.59        11.70        61.22        20.81        55.43         6.58 
TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6I 
        2.66        28.41        16.14 

  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                           0.1                            0.0 
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                         122.1                          122.3 
  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE 
                        13.365                         15.520 
[1] "0.1 - 122.1 (13.4)" "0.0 - 122.3 (15.5)"
[1] "hr=" "1.3"
D37V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 37(20Q13.2) MUTATED         7       14       29       19        51
  AMP PEAK 37(20Q13.2) WILD-TYPE       3        7       18       14        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 37(20Q13.2) MUTATED          59        21         69         48
  AMP PEAK 37(20Q13.2) WILD-TYPE        28         7         26         24
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 37(20Q13.2) MUTATED           27       31         4
  AMP PEAK 37(20Q13.2) WILD-TYPE         19       18         0
D37V3, multiclass
            clus
vv           AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  STAGE I                               7                              3
  STAGE IA                             14                              7
  STAGE IB                             29                             18
  STAGE II                             19                             14
  STAGE IIA                            51                             36
  STAGE IIB                            59                             28
  STAGE III                            21                              7
  STAGE IIIA                           69                             26
  STAGE IIIB                           48                             24
  STAGE IIIC                           27                             19
  STAGE IV                             31                             18
  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 37(20Q13.2) MUTATED      37  87 197  73
  AMP PEAK 37(20Q13.2) WILD-TYPE    18  49  86  51
D37V4, multiclass
       clus
vv      AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  T0+T1                           37                             18
  T2                              87                             49
  T3                             197                             86
  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 37(20Q13.2) MUTATED   123 135  68  60
  AMP PEAK 37(20Q13.2) WILD-TYPE  84  52  30  36
D37V5, multiclass
    clus
vv   AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  N0                          123                             84
  N1                          135                             52
  N2                           68                             30
  N3                           60                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                                cls
clus                               0   1
  AMP PEAK 37(20Q13.2) MUTATED   342  25
  AMP PEAK 37(20Q13.2) WILD-TYPE 182  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(20Q13.2) MUTATED    342   25
  AMP PEAK 37(20Q13.2) WILD-TYPE  182   14
   clus
vv  AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  0                          342                            182
  1                           25                             14
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(20Q13.2) MUTATED   107 309
  AMP PEAK 37(20Q13.2) WILD-TYPE  78 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(20Q13.2) MUTATED    107  309
  AMP PEAK 37(20Q13.2) WILD-TYPE   78  131
        clus
vv       AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  FEMALE                          107                             78
  MALE                            309                            131
[1] 2 2
[1] FALSE
D37V8, binary
                                cls
clus                               0   1
  AMP PEAK 37(20Q13.2) MUTATED   300  75
  AMP PEAK 37(20Q13.2) WILD-TYPE 145  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(20Q13.2) MUTATED    300   75
  AMP PEAK 37(20Q13.2) WILD-TYPE  145   44
     clus
vv    AMP PEAK 37(20Q13.2) MUTATED AMP PEAK 37(20Q13.2) WILD-TYPE
  NO                           300                            145
  YES                           75                             44
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 37(20Q13.2) MUTATED      89                        11
  AMP PEAK 37(20Q13.2) WILD-TYPE    45                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 37(20Q13.2) MUTATED                                           1
  AMP PEAK 37(20Q13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 37(20Q13.2) MUTATED     254
  AMP PEAK 37(20Q13.2) WILD-TYPE   138
D37V11, multiclass
                                           clus
vv                                          AMP PEAK 37(20Q13.2) MUTATED
  ASIAN                                                               89
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              254
                                           clus
vv                                          AMP PEAK 37(20Q13.2) WILD-TYPE
  ASIAN                                                                 45
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                                cls
clus                               0   1
  AMP PEAK 37(20Q13.2) MUTATED     7 259
  AMP PEAK 37(20Q13.2) WILD-TYPE   4 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(20Q13.2) MUTATED      7  259
  AMP PEAK 37(20Q13.2) WILD-TYPE    4  145
                        clus
vv                       AMP PEAK 37(20Q13.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          259
                        clus
vv                       AMP PEAK 37(20Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            145
[1] 2 2
[1] FALSE

Clustering(38) Variable = AMP PEAK 38(XQ28) MUTATION ANALYSIS
D38V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 38(XQ28) MUTATED    87  63
  AMP PEAK 38(XQ28) WILD-TYPE 267 182
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                        150                         449 
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                         63                         182 
$`AMP PEAK 38(XQ28) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OI TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00        19.99        20.02 
TCGA-CG-4460 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GO 
       21.99         0.23        27.35        14.30         5.92        16.24 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       35.21        20.78         3.88         0.53        17.03        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A93C 
       12.82         9.96         4.67       122.10        44.75        23.18 
TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A8NK TCGA-L5-A8NQ 
       30.25        47.93        18.35         1.38        13.55        21.37 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P 
       10.36         5.92        10.45        12.66        12.43        12.33 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.38        12.59        12.62        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I1 
       22.39        13.22        25.25        12.00        13.18        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A8W5 
        0.13        12.85        12.26         8.02        16.31        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EU 
        2.89        12.69         5.29        15.35         8.98        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B 
        8.12        33.70        18.18        52.27        46.19        11.24 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ 
       15.91        25.08        14.37         3.42         2.10        19.73 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-6458 
       11.70        11.01         9.44         6.61         4.64        19.33 
TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8486 
       40.21        18.15        14.43        13.08         3.32        20.22 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4IY 
       26.73        31.96         9.86        13.87        34.98        12.89 
TCGA-BR-A4J2 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 
       14.17         1.15        21.44        12.10        12.76         7.17 
TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-4472 
        6.58        20.02         8.05        54.08         7.07        12.00 
TCGA-CG-5717 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 
        6.97        20.91        18.54        17.19        15.22        15.98 
TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 
       12.33        14.66        36.43        11.24        20.32        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-A9TM 
       19.96         0.62         7.99        72.23         3.48         6.21 
TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       52.21        24.39        22.82        24.30        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 
       24.20        22.75        25.81        23.80         3.45         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-VQ-A8DT 
       13.35         6.44        36.95        45.67        18.21        48.79 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q 
        7.73        46.26        14.33        21.83        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6A 
       32.88         1.71        55.56        66.81        43.66        38.93 

$`AMP PEAK 38(XQ28) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         8.94         4.70        22.82         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       35.97        27.12         5.16        47.05        22.98        79.07 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24        20.15         9.86        26.93        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55         7.63        13.94         8.94         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
        7.69        33.27         0.85         2.63        20.12        18.64 
TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FD 
        9.30         0.79        14.86        14.50        12.16        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E 
        3.68        41.52        47.38        21.70        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       24.03         6.28         3.16         0.30        26.33        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-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
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-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49O 
       13.41        83.24        52.57        46.09        10.85        13.41 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15        15.35        13.25        12.46        12.76        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV 
       15.52        11.54        12.33         4.47        12.33        10.52 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-M9-A5M8 
       12.23        12.03        12.33        13.38        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         7.59         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
       53.95         9.30         2.30         7.00        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       16.44         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 
        1.55        28.11        18.05         9.17        18.21        41.23 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK 
        1.32         2.66        58.03        26.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-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        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        39.78        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40         6.18        31.10         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
        6.28         7.53        24.79        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        34.13         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98         0.72         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
       32.52        13.51         0.46        20.65        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       11.21        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
        6.31        12.30        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 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        7.99         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
        0.00         9.01        18.97        30.97        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-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       25.71        12.66        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.85        13.35        10.26        12.79        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        18.21        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.31        11.44        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
        7.13        14.47        21.27        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.52        77.29        63.06        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        18.15        28.96        22.32        21.07         0.76 
TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        5.59         3.25        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       33.40        36.36        18.81        18.38        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-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        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A91W 
       73.41        39.45        11.70        61.22        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.50         9.73         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        6.58         5.72        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        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                       0.13                        0.00 
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                      122.1                       122.3 
  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE 
                      14.94                       13.51 
[1] "0.1 - 122.1 (14.9)" "0.0 - 122.3 (13.5)"
[1] "hr=" "1"  
D38V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 38(XQ28) MUTATED         2        7        8        5        26
  AMP PEAK 38(XQ28) WILD-TYPE       8       14       39       28        61
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 38(XQ28) MUTATED          27         6         19         18
  AMP PEAK 38(XQ28) WILD-TYPE        60        22         76         54
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 38(XQ28) MUTATED            9       13         2
  AMP PEAK 38(XQ28) WILD-TYPE         37       36         2
D38V3, multiclass
            clus
vv           AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  STAGE I                            2                           8
  STAGE IA                           7                          14
  STAGE IB                           8                          39
  STAGE II                           5                          28
  STAGE IIA                         26                          61
  STAGE IIB                         27                          60
  STAGE III                          6                          22
  STAGE IIIA                        19                          76
  STAGE IIIB                        18                          54
  STAGE IIIC                         9                          37
  STAGE IV                          13                          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 38(XQ28) MUTATED      16  36  71  25
  AMP PEAK 38(XQ28) WILD-TYPE    39 100 212  99
D38V4, multiclass
       clus
vv      AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  T0+T1                        16                          39
  T2                           36                         100
  T3                           71                         212
  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 38(XQ28) MUTATED    54  48  24  20
  AMP PEAK 38(XQ28) WILD-TYPE 153 139  74  76
D38V5, multiclass
    clus
vv   AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  N0                        54                         153
  N1                        48                         139
  N2                        24                          74
  N3                        20                          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"
D38V6, binary
                             cls
clus                            0   1
  AMP PEAK 38(XQ28) MUTATED   125   9
  AMP PEAK 38(XQ28) WILD-TYPE 399  30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 38(XQ28) MUTATED    125    9
  AMP PEAK 38(XQ28) WILD-TYPE  399   30
   clus
vv  AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  0                       125                         399
  1                         9                          30
[1] 2 2
[1] FALSE
D38V7, binary
                             cls
clus                            0   1
  AMP PEAK 38(XQ28) MUTATED    37 118
  AMP PEAK 38(XQ28) WILD-TYPE 148 322
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 38(XQ28) MUTATED     37  118
  AMP PEAK 38(XQ28) WILD-TYPE  148  322
        clus
vv       AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  FEMALE                        37                         148
  MALE                         118                         322
[1] 2 2
[1] FALSE
D38V8, binary
                             cls
clus                            0   1
  AMP PEAK 38(XQ28) MUTATED   110  30
  AMP PEAK 38(XQ28) WILD-TYPE 335  89
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 38(XQ28) MUTATED    110   30
  AMP PEAK 38(XQ28) WILD-TYPE  335   89
     clus
vv    AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  NO                        110                         335
  YES                        30                          89
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  AMP PEAK 38(XQ28) MUTATED      44                         6
  AMP PEAK 38(XQ28) WILD-TYPE    90                        11
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 38(XQ28) MUTATED                                           0    90
  AMP PEAK 38(XQ28) WILD-TYPE                                         1   302
D38V11, multiclass
                                           clus
vv                                          AMP PEAK 38(XQ28) MUTATED
  ASIAN                                                            44
  BLACK OR AFRICAN AMERICAN                                         6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            90
                                           clus
vv                                          AMP PEAK 38(XQ28) WILD-TYPE
  ASIAN                                                              90
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             302
[1] 4 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, binary
                             cls
clus                            0   1
  AMP PEAK 38(XQ28) MUTATED     5 102
  AMP PEAK 38(XQ28) WILD-TYPE   6 302
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 38(XQ28) MUTATED      5  102
  AMP PEAK 38(XQ28) WILD-TYPE    6  302
                        clus
vv                       AMP PEAK 38(XQ28) MUTATED AMP PEAK 38(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             5                           6
  NOT HISPANIC OR LATINO                       102                         302
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   114  90
  DEL PEAK  1(1P36.11) WILD-TYPE 240 155
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           204                            395 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            90                            155 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-CG-4444 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GH 
       35.97        47.05        16.24         9.86        27.35        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A4P3 TCGA-IG-A4QS 
       32.45         7.69        33.27        35.21        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A625 TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43H 
        0.53        12.82       122.10        47.38        23.18         0.30 
TCGA-L5-A4OF TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       26.33         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH 
        7.43         2.60         7.40         3.02        55.50        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49R 
       16.47        13.22         5.49        13.41         5.92        13.38 
TCGA-LN-A49W TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ 
       13.25        12.33        25.25        12.00        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 
       12.33        12.85         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 
        2.30        20.38         3.42        16.44         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN 
       33.70        52.27        25.08        14.37         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 
       19.73        58.03        26.70        11.01         9.44        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 
        4.08         9.67         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        33.21        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        26.73        24.79         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        7.53        34.98        20.65        20.42         1.15        21.44 
TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
       13.02        12.59         7.17        12.30        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82         6.31        12.30        11.31        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-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
       14.01        29.98        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        20.91        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        22.29        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-7133 
        7.99        11.38        17.06        13.58         5.52        63.06 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GF TCGA-HU-A4GP 
        1.51         5.92        28.96        22.82        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        23.80        33.40        15.75        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT 
       37.64        36.95        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-A91A TCGA-VQ-A91Q TCGA-VQ-A91Y 
       17.85         1.87        13.35        39.45        20.81         9.73 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 
       55.56         4.54        66.81        21.04        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       43.66        38.93        32.94        17.13        12.43         0.79 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        34.85        18.28        19.99        22.82        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX 
        5.16        20.02        21.99        22.98        79.07         0.23 
TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3Y9 
       20.15        26.93        25.78         5.92         4.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.78         2.63        20.12         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D 
       44.75        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-A4OH 
       25.22        24.03         6.28         3.16        30.25        32.61 
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-A88S TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK 
       15.48        25.12         3.75         2.66        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76        21.37         8.71        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85        10.36        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.15        15.35        12.59        12.62        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        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A7HX TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR 
       12.23        13.38        13.18         0.13        12.03        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.82        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB 
       53.95         9.30        15.78        12.69         7.00         5.29 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       15.35        25.81        18.31        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JD 
       11.24         9.17        15.91        18.21        41.23         3.42 
TCGA-Z6-A8JE TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
        2.10        11.70        19.56         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4280 
        4.64         7.43        30.90         4.08         9.34         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-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 
       14.79         7.36        25.05         3.72        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 
       13.51         0.46        16.14         5.13        13.41        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG 
       12.33        12.39        12.59        12.43        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4440 
       11.77        12.62        27.02        15.95         1.02         4.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5717 
       12.03         0.00         9.01        18.97        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
       36.00         0.99         6.02         0.99       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85        13.35 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       15.98        12.36        11.31        16.80        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         7.13        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        0.56         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        18.15        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 
       20.25         0.26         2.10        29.00        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        11.70        13.51         2.53         5.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60        11.05         5.13        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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.79        48.79         5.46        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       38.14        37.22        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       73.41        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        42.64        60.85         9.50         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 
       55.43         6.58         5.72         2.66        42.54        28.41 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        17.26 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           0.3                            0.0 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        13.235                         14.430 
[1] "0.3 - 122.3 (13.2)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1.2"
D39V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         5        3       17       12        28
  DEL PEAK  1(1P36.11) WILD-TYPE       5       18       30       21        59
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          29        15         31         24
  DEL PEAK  1(1P36.11) WILD-TYPE        58        13         64         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         37       32         2
D39V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                              3                             18
  STAGE IB                             17                             30
  STAGE II                             12                             21
  STAGE IIA                            28                             59
  STAGE IIB                            29                             58
  STAGE III                            15                             13
  STAGE IIIA                           31                             64
  STAGE IIIB                           24                             48
  STAGE IIIC                            9                             37
  STAGE IV                             17                             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  1(1P36.11) MUTATED      19  47 100  32
  DEL PEAK  1(1P36.11) WILD-TYPE    36  89 183  92
D39V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                           19                             36
  T2                              47                             89
  T3                             100                            183
  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    63  69  34  28
  DEL PEAK  1(1P36.11) WILD-TYPE 144 118  64  68
D39V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           63                            144
  N1                           69                            118
  N2                           34                             64
  N3                           28                             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"
D39V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   173  13
  DEL PEAK  1(1P36.11) WILD-TYPE 351  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    173   13
  DEL PEAK  1(1P36.11) WILD-TYPE  351   26
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          173                            351
  1                           13                             26
[1] 2 2
[1] FALSE
D39V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    54 156
  DEL PEAK  1(1P36.11) WILD-TYPE 131 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     54  156
  DEL PEAK  1(1P36.11) WILD-TYPE  131  284
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           54                            131
  MALE                            156                            284
[1] 2 2
[1] FALSE
D39V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   143  43
  DEL PEAK  1(1P36.11) WILD-TYPE 302  76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    143   43
  DEL PEAK  1(1P36.11) WILD-TYPE  302   76
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           143                            302
  YES                           43                             76
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.11) MUTATED      42                         7
  DEL PEAK  1(1P36.11) WILD-TYPE    92                        10
                                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     126
  DEL PEAK  1(1P36.11) WILD-TYPE   266
D39V11, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                               42
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              126
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                                 92
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                266
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3 116
  DEL PEAK  1(1P36.11) WILD-TYPE   8 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3  116
  DEL PEAK  1(1P36.11) WILD-TYPE    8  288
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    90  62
  DEL PEAK  2(1P13.2) WILD-TYPE 264 183
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          152                           447 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           62                           183 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-CG-4475 
        8.94        24.00         4.70         0.36        35.97        22.98 
TCGA-EQ-A4SO TCGA-MX-A663 TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GQ 
       16.24         9.86        14.30         7.63        13.94         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 
       32.45         7.69        33.27        35.21         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A8O2 TCGA-JY-A6FE TCGA-L5-A43H 
        3.88         0.53         0.79         4.67         3.68         0.30 
TCGA-L5-A4OH TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
       32.61         4.90        29.00         7.13         7.43        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        2.60         7.40        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 
       16.47        13.41         5.92        13.25        12.59        12.59 
TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ 
       11.54        12.33        25.25        10.52        12.00        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       12.33        13.38        13.18        12.85        12.26        33.11 
TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RC 
        7.59        53.95         2.89         2.30        20.38         3.42 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-AA4D TCGA-XP-A8T8 
        9.27         8.98        12.43         8.12        46.19        14.37 
TCGA-Z6-A9VB TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-7704 
        1.32        11.01         9.44         9.67        17.29        35.24 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8483 
        3.45        33.21         2.66         2.20        14.04         5.39 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IY 
        9.21        24.79         9.86         8.22        34.98        12.89 
TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
        0.66        20.42         1.15        21.44        13.02        13.35 
TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
        7.17        12.59        15.39        12.07        12.82         6.31 
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-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 
       18.97        12.03         4.01        20.91        20.55        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 
       17.19        10.26        15.22        12.79        24.72        19.50 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31        20.32        15.65        19.96         0.62         7.99 
TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD 
       19.53         5.52         1.51        28.96        22.82        22.75 
TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7ZE TCGA-R5-A805 
       33.40        13.35         2.53        37.64        18.21         9.24 
TCGA-RD-A7BT TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8P5 
        8.61         0.92        48.79         5.46        13.25         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A91A TCGA-VQ-A91N 
       22.19         2.70        17.85         9.27        39.45        18.74 
TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 
       42.64        55.56         4.54        21.04        11.24        18.41 
TCGA-VQ-AA6B TCGA-VQ-AA6K 
       32.94        12.43 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         4.31        19.99 
TCGA-L5-A88T TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
       22.82        27.12         5.16        20.02        47.05        21.99 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
       79.07         0.23        20.15        27.35        26.93        25.78 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3Y9 
       31.27        58.55         5.92         8.94        16.24         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       20.78        20.12         9.30        17.03        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA 
        9.96        14.86        14.50        12.16       122.10        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D 
       68.02        41.52        47.38        21.70        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       25.22        24.03         6.28         3.16        30.25        26.33 
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-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NK 
        3.16        58.59        25.12         3.75         3.02        13.55 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
       13.22         7.76         5.49        21.37         8.71        83.24 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 
       12.59        12.62        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 
       12.85        15.52        12.33        13.22         4.47        12.23 
TCGA-LN-A7HY TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.03         0.13        12.03         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EO 
       12.69         7.00         5.29        16.44        15.35        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09        22.82         1.55        18.31        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       18.21        25.08        41.23         3.42         2.10         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       19.73        58.03        26.70        11.70        19.56         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       21.90         9.21        36.16        35.84        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32        28.73         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        29.42        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 
       14.79         7.36        25.05         3.72        25.18        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
        7.53        26.73        31.96        32.58        20.88        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51         0.46        20.65        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.15        13.18        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
       12.59        12.53        12.33        12.30        12.39        11.64 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        12.43        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       12.62        20.02        27.02        15.95         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        19.07        12.03         0.00         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       19.13        18.84        18.61        17.85        13.35        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       12.36        11.31        12.33        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-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 
       22.29         8.38         4.34         7.13        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-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        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         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        18.38        12.46        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       13.51         5.56        63.62        36.95         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67         8.52        74.53         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        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PP 
       46.26        16.31         2.50        12.79         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50         9.73         9.04         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 
        6.58         5.72        66.81         2.66        42.54        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          0.3                           0.0 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        55.56                        122.30 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        12.59                         15.35 
[1] "0.3 - 55.6 (12.6)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.2) MUTATED         2        2       10        7        28
  DEL PEAK  2(1P13.2) WILD-TYPE       8       19       37       26        59
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          23        12         23         18
  DEL PEAK  2(1P13.2) WILD-TYPE        64        16         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         42       38         3
D40V3, multiclass
            clus
vv           DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             2                            19
  STAGE IB                            10                            37
  STAGE II                             7                            26
  STAGE IIA                           28                            59
  STAGE IIB                           23                            64
  STAGE III                           12                            16
  STAGE IIIA                          23                            72
  STAGE IIIB                          18                            54
  STAGE IIIC                           4                            42
  STAGE IV                            11                            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  2(1P13.2) MUTATED      12  32  82  21
  DEL PEAK  2(1P13.2) WILD-TYPE    43 104 201 103
D40V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                          12                            43
  T2                             32                           104
  T3                             82                           201
  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    52  47  30  15
  DEL PEAK  2(1P13.2) WILD-TYPE 155 140  68  81
D40V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          52                           155
  N1                          47                           140
  N2                          30                            68
  N3                          15                            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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED   131   9
  DEL PEAK  2(1P13.2) WILD-TYPE 393  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED    131    9
  DEL PEAK  2(1P13.2) WILD-TYPE  393   30
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                         131                           393
  1                           9                            30
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    36 120
  DEL PEAK  2(1P13.2) WILD-TYPE 149 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     36  120
  DEL PEAK  2(1P13.2) WILD-TYPE  149  320
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          36                           149
  MALE                           120                           320
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED   108  32
  DEL PEAK  2(1P13.2) WILD-TYPE 337  87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED    108   32
  DEL PEAK  2(1P13.2) WILD-TYPE  337   87
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                          108                           337
  YES                          32                            87
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P13.2) MUTATED      37                         3
  DEL PEAK  2(1P13.2) WILD-TYPE    97                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1P13.2) MUTATED                                           1    93
  DEL PEAK  2(1P13.2) WILD-TYPE                                         0   299
D40V11, multiclass
                                           clus
vv                                          DEL PEAK  2(1P13.2) MUTATED
  ASIAN                                                              37
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              93
                                           clus
vv                                          DEL PEAK  2(1P13.2) WILD-TYPE
  ASIAN                                                                97
  BLACK OR AFRICAN AMERICAN                                            14
  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"
D40V12, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     1  96
  DEL PEAK  2(1P13.2) WILD-TYPE  10 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1   96
  DEL PEAK  2(1P13.2) WILD-TYPE   10  308
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           308
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    22  22
  DEL PEAK  3(1Q44) WILD-TYPE 332 223
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         44                         555 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         22                         223 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A8NG TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-JY-A6F8 
       18.28        24.00        35.97         4.21         3.88       122.10 
TCGA-L5-A4OJ TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A4A5 
       21.01        83.24         5.92        13.41        12.46        22.39 
TCGA-R6-A6DQ TCGA-R6-A6Y0 TCGA-VR-A8ER TCGA-VR-AA7D TCGA-B7-A5TN TCGA-BR-6456 
        7.59        53.95        12.43         9.17         9.44        17.29 
TCGA-BR-7704 TCGA-BR-8362 TCGA-BR-A452 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-A486 
       35.24        13.08         7.53        20.65        13.18         6.31 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4469 
       12.43        12.20         1.02        14.01        18.97         7.07 
TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HU-8604 TCGA-HU-A4GP 
       12.03        20.55        14.66        15.65        22.82         8.98 
TCGA-HU-A4H0 TCGA-IN-8663 TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
        2.10         3.39        11.70         2.53         5.56        37.64 
TCGA-VQ-A8PM TCGA-VQ-A91V 
        1.87        42.64 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
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-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24        32.45         7.69        33.27        35.21         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-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-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       41.52        47.38        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-A4OF 
       24.03         6.28         3.16        30.25         0.30        26.33 
TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        47.93        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         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-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS 
       13.22         7.76         5.49        21.37         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M 
       52.57        46.09        10.85        10.36        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.85        12.26        33.11         7.82         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       16.31         7.04        38.40         6.35         9.30        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        2.89         2.30        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-A8EO 
        3.42        16.44        15.35         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        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 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
        2.10         1.32         2.66        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 
       11.70        19.56        11.01         9.47         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       37.25        14.43        11.44         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
        8.22        10.68        34.13        13.87         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.42         1.15        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 
       12.39        12.59        11.64        15.39        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       12.43        12.30        11.31        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       12.62        20.02         3.02        27.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        0.00         9.01        12.00        30.97         6.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       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        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       26.43        11.24        11.31        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
        8.38         4.34        19.96         7.13         0.62         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-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        0.56         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       20.25         0.26        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81        18.38        12.46        13.35        19.53         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        10.62        15.75        13.51 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.46        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       37.41        38.14        37.22         7.73        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       46.26        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
        9.50         9.73        55.56         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        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       42.54        11.24        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK  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 
                      12.77                       14.07 
[1] "1.0 - 122.1 (12.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D41V2, 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       8       21       45       32        77
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1Q44) MUTATED           5         3          6          5
  DEL PEAK  3(1Q44) WILD-TYPE        82        25         89         67
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  3(1Q44) MUTATED            4        4         0
  DEL PEAK  3(1Q44) WILD-TYPE         42       45         4
D41V3, multiclass
            clus
vv           DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                            2                           8
  STAGE IA                           0                          21
  STAGE IB                           2                          45
  STAGE II                           1                          32
  STAGE IIA                         10                          77
  STAGE IIB                          5                          82
  STAGE III                          3                          25
  STAGE IIIA                         6                          89
  STAGE IIIB                         5                          67
  STAGE IIIC                         4                          42
  STAGE IV                           4                          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  3(1Q44) MUTATED       2   8  25   8
  DEL PEAK  3(1Q44) WILD-TYPE    53 128 258 116
D41V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         2                          53
  T2                            8                         128
  T3                           25                         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  3(1Q44) MUTATED    15  10   8   9
  DEL PEAK  3(1Q44) WILD-TYPE 192 177  90  87
D41V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        15                         192
  N1                        10                         177
  N2                         8                          90
  N3                         9                          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"
D41V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    39   2
  DEL PEAK  3(1Q44) WILD-TYPE 485  37
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     39    2
  DEL PEAK  3(1Q44) WILD-TYPE  485   37
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        39                         485
  1                         2                          37
[1] 2 2
[1] FALSE
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    13  33
  DEL PEAK  3(1Q44) WILD-TYPE 172 407
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     13   33
  DEL PEAK  3(1Q44) WILD-TYPE  172  407
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        13                         172
  MALE                          33                         407
[1] 2 2
[1] FALSE
D41V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    31   8
  DEL PEAK  3(1Q44) WILD-TYPE 414 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     31    8
  DEL PEAK  3(1Q44) WILD-TYPE  414  111
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                         31                         414
  YES                         8                         111
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(1Q44) MUTATED      13                         0
  DEL PEAK  3(1Q44) WILD-TYPE   121                        17
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(1Q44) MUTATED                                           0    23
  DEL PEAK  3(1Q44) WILD-TYPE                                         1   369
D41V11, multiclass
                                           clus
vv                                          DEL PEAK  3(1Q44) MUTATED
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                         0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            23
                                           clus
vv                                          DEL PEAK  3(1Q44) WILD-TYPE
  ASIAN                                                             121
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             369
[1] 4 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, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     0  28
  DEL PEAK  3(1Q44) WILD-TYPE  11 376
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      0   28
  DEL PEAK  3(1Q44) WILD-TYPE   11  376
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                          11
  NOT HISPANIC OR LATINO                        28                         376
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  4(1Q44) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q44) MUTATED    23  19
  DEL PEAK  4(1Q44) WILD-TYPE 331 226
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         42                         557 
  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE 
                         19                         226 
$`DEL PEAK  4(1Q44) MUTATED`
TCGA-L5-A4OE TCGA-L5-A8NG TCGA-IG-A4QS TCGA-IG-A6QS TCGA-L5-A4OJ TCGA-L5-A4OO 
       24.00        35.97         3.88         9.96        21.01         3.32 
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         6.31        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        22.82         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        37.22        42.64         5.72 

$`DEL PEAK  4(1Q44) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82         0.36        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
        0.23        20.15         9.86        27.35        26.93        25.78 
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-IG-A3I8 
        8.94        16.24         4.21        32.45         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         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-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-A93C 
       68.02         3.68        41.52        47.38        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-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        26.33        32.61        47.93        18.35         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-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
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-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-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M 
       13.41        52.57        46.09        10.85        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       12.33        25.25        10.52        12.23        12.03        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         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 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       22.82         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
       18.18        52.27        46.19        18.05        11.24        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        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-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-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-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       33.63        39.78        18.15        15.32        28.73         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        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 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       11.64        15.39        12.07        12.82        12.43        12.30 
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        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       10.26        15.22        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        22.29         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        28.96        22.32        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36         3.45        18.81        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG 
       15.75        13.51         5.56        63.62        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       71.38        57.44         8.94        35.61        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        43.36        21.73        37.41        38.14         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88         1.71        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.04         2.01        55.43         4.54         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       16.14        27.55        12.43        17.26         0.79 

  DEL PEAK  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 
                     13.245                      14.040 
[1] "0.7 - 83.2 (13.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D42V2, 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       8       21       46       32        77
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q44) MUTATED           7         2          3          6
  DEL PEAK  4(1Q44) WILD-TYPE        80        26         92         66
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  4(1Q44) MUTATED            6        2         0
  DEL PEAK  4(1Q44) WILD-TYPE         40       47         4
D42V3, multiclass
            clus
vv           DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  STAGE I                            2                           8
  STAGE IA                           0                          21
  STAGE IB                           1                          46
  STAGE II                           1                          32
  STAGE IIA                         10                          77
  STAGE IIB                          7                          80
  STAGE III                          2                          26
  STAGE IIIA                         3                          92
  STAGE IIIB                         6                          66
  STAGE IIIC                         6                          40
  STAGE IV                           2                          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  4(1Q44) MUTATED       2   9  22   8
  DEL PEAK  4(1Q44) WILD-TYPE    53 127 261 116
D42V4, multiclass
       clus
vv      DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  T0+T1                         2                          53
  T2                            9                         127
  T3                           22                         261
  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 193 177  92  86
D42V5, multiclass
    clus
vv   DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  N0                        14                         193
  N1                        10                         177
  N2                         6                          92
  N3                        10                          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"
D42V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    37   1
  DEL PEAK  4(1Q44) WILD-TYPE 487  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     37    1
  DEL PEAK  4(1Q44) WILD-TYPE  487   38
   clus
vv  DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  0                        37                         487
  1                         1                          38
[1] 2 2
[1] FALSE
D42V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    14  29
  DEL PEAK  4(1Q44) WILD-TYPE 171 411
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     14   29
  DEL PEAK  4(1Q44) WILD-TYPE  171  411
        clus
vv       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  FEMALE                        14                         171
  MALE                          29                         411
[1] 2 2
[1] FALSE
D42V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED    29   8
  DEL PEAK  4(1Q44) WILD-TYPE 416 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED     29    8
  DEL PEAK  4(1Q44) WILD-TYPE  416  111
     clus
vv    DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  NO                         29                         416
  YES                         8                         111
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(1Q44) MUTATED      11                         0
  DEL PEAK  4(1Q44) WILD-TYPE   123                        17
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(1Q44) MUTATED                                           0    27
  DEL PEAK  4(1Q44) WILD-TYPE                                         1   365
D42V11, 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                                                             123
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             365
[1] 4 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, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q44) MUTATED     0  30
  DEL PEAK  4(1Q44) WILD-TYPE  11 374
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q44) MUTATED      0   30
  DEL PEAK  4(1Q44) WILD-TYPE   11  374
                        clus
vv                       DEL PEAK  4(1Q44) MUTATED DEL PEAK  4(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             0                          11
  NOT HISPANIC OR LATINO                        30                         374
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    70  53
  DEL PEAK  5(2Q22.1) WILD-TYPE 284 192
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          123                           476 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           53                           192 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-MX-A663 
       24.00         5.16        47.05        22.98        16.24         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 
       27.35        26.93        58.55         4.21        33.27         0.85 
TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        2.63        20.12        18.64         0.53        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG 
        9.96         4.67        12.16        44.75        68.02        41.52 
TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OS TCGA-L5-A4OX TCGA-L5-A88Z TCGA-L5-A893 
        3.16         0.30        58.59         7.43         7.40         3.02 
TCGA-L5-A8NK TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49Y TCGA-LN-A4MQ 
       13.55        52.57        10.36        10.45        12.46        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-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6XG TCGA-R6-A6Y0 
       12.33        13.18         0.13        12.85        38.40        53.95 
TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
        2.89        20.38         5.29        12.43        18.31         8.12 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       33.70        18.18        52.27        11.24        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-BR-4183 
       41.23        14.37         3.42         1.32         2.66         6.61 
TCGA-BR-4188 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8369 
        7.43        19.33         9.17        28.73         0.69        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8687 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-8534 
        5.39        25.18         8.22         0.66        20.65        12.07 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4300 TCGA-CG-4466 TCGA-CG-5720 
       12.82         6.31        12.43        20.02        18.97         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        20.91        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        22.29         0.62 
TCGA-F1-A72C TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD 
       11.38        63.06        26.47        22.75         6.58        33.40 
TCGA-IN-A6RI TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7ZE 
       18.38         6.51        15.75        37.64        36.95        18.21 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E0 
       16.67       115.69        35.61         0.92        13.02        18.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 
        7.73         2.70        11.70        18.74        55.56         9.04 
TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A 
       42.54        43.66        38.93 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
        4.70        19.99        22.82         0.36        35.97        27.12 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF 
       20.02        21.99        79.07         0.23        20.15        25.78 
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-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS 
       16.24        32.45         7.69        35.21        20.78         3.88 
TCGA-IG-A4QT TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 
        9.30        23.41        12.82        14.86        14.50       122.10 
TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
        3.68        47.38        21.70        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         6.28        30.25        26.33        32.61        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-A88S TCGA-L5-A88V TCGA-L5-A88W 
        4.90        29.00         7.13        15.48         2.60        25.12 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        3.75        55.50         2.66        12.92        13.48        16.47 
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-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       83.24        46.09        10.85         5.92        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        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-A5U7 
       22.39        12.85        15.52        11.54        13.22        25.25 
TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.03        13.38        12.03        12.26        33.11         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        16.31         7.04         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RC 
        9.30        15.78         2.30        12.69         7.00         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
       16.44        15.35         9.27         8.98        25.81        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D 
       22.82         1.55        28.11        46.19        18.05         9.17 
TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
       18.21         2.10        19.73        58.03        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-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       35.84        33.63        39.78        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        9.07        29.56        33.21        37.25        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17         0.53        28.34        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 
       12.39        12.59        11.64        15.39        12.43        12.30 
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        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5728 
       36.00         1.02         6.02         0.99        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
        4.01        69.04        21.07         7.99        25.71        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         7.99        14.47        72.23 
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-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       59.54         5.03        13.58         0.56         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        52.21        30.51         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       23.84        23.80        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.44         6.74        12.59        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        74.53         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-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-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79        48.79         5.46        13.25        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19         2.50        12.79        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        73.41        39.45        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         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        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       21.04         2.66        11.24        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         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 
                       13.180                        14.025 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q22.1) MUTATED         3        2        9        5        26
  DEL PEAK  5(2Q22.1) WILD-TYPE       7       19       38       28        61
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q22.1) MUTATED          18         6         19         12
  DEL PEAK  5(2Q22.1) WILD-TYPE        69        22         76         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  5(2Q22.1) MUTATED            7       11         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         39       38         4
D43V3, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                             2                            19
  STAGE IB                             9                            38
  STAGE II                             5                            28
  STAGE IIA                           26                            61
  STAGE IIB                           18                            69
  STAGE III                            6                            22
  STAGE IIIA                          19                            76
  STAGE IIIB                          12                            60
  STAGE IIIC                           7                            39
  STAGE IV                            11                            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  5(2Q22.1) MUTATED      10  32  58  21
  DEL PEAK  5(2Q22.1) WILD-TYPE    45 104 225 103
D43V4, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                          10                            45
  T2                             32                           104
  T3                             58                           225
  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    46  42  18  16
  DEL PEAK  5(2Q22.1) WILD-TYPE 161 145  80  80
D43V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          46                           161
  N1                          42                           145
  N2                          18                            80
  N3                          16                            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"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED   107   8
  DEL PEAK  5(2Q22.1) WILD-TYPE 417  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED    107    8
  DEL PEAK  5(2Q22.1) WILD-TYPE  417   31
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                         107                           417
  1                           8                            31
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    37  89
  DEL PEAK  5(2Q22.1) WILD-TYPE 148 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     37   89
  DEL PEAK  5(2Q22.1) WILD-TYPE  148  351
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          37                           148
  MALE                            89                           351
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    88  31
  DEL PEAK  5(2Q22.1) WILD-TYPE 357  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     88   31
  DEL PEAK  5(2Q22.1) WILD-TYPE  357   88
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           88                           357
  YES                          31                            88
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q22.1) MUTATED      29                         4
  DEL PEAK  5(2Q22.1) WILD-TYPE   105                        13
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q22.1) MUTATED                                           0    75
  DEL PEAK  5(2Q22.1) WILD-TYPE                                         1   317
D43V11, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q22.1) MUTATED
  ASIAN                                                              29
  BLACK OR AFRICAN AMERICAN                                           4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK  5(2Q22.1) WILD-TYPE
  ASIAN                                                               105
  BLACK OR AFRICAN AMERICAN                                            13
  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"
D43V12, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     4  73
  DEL PEAK  5(2Q22.1) WILD-TYPE   7 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      4   73
  DEL PEAK  5(2Q22.1) WILD-TYPE    7  331
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          73
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           331
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK  6(2Q32.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q32.1) MUTATED    48  36
  DEL PEAK  6(2Q32.1) WILD-TYPE 306 209
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           84                           515 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           36                           209 
$`DEL PEAK  6(2Q32.1) MUTATED`
TCGA-L5-A88Y TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-IG-A3Y9 
        0.36        47.05         9.86        27.35        26.93         0.85 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-L5-A43H TCGA-L5-A4OS 
       20.12        18.64         0.79        68.02         0.30        58.59 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NV TCGA-LN-A49O TCGA-LN-A49Y 
        3.02        16.47        13.55        52.57        13.41        12.46 
TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-R6-A8W8 
       12.33        10.52        12.23        13.18        12.33         2.89 
TCGA-R6-A8WC TCGA-VR-A8Q7 TCGA-ZR-A9CJ TCGA-BR-4188 TCGA-BR-6456 TCGA-BR-6458 
        2.30        52.27        19.73         7.43        17.29        19.33 
TCGA-BR-6565 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8367 
        9.17        37.25         0.69         9.60        29.42        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 
        4.31        14.04         3.32         7.53        32.58         8.22 
TCGA-BR-A4PD TCGA-CD-8525 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 
       20.65        12.59        11.64        12.07        12.82         6.31 
TCGA-CG-4300 TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5725 
       20.02         0.00        12.00         0.99        12.03        15.02 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6F0 
       12.66        20.91        17.19        18.21        14.66        22.29 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G3 TCGA-HU-A4GD TCGA-HU-A4GU 
       63.06        26.47         5.92         5.59        22.75         6.58 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-AB1V TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7ZE 
       33.40        18.38        15.75        36.95        14.04        18.21 
TCGA-RD-A7C1 TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PK 
       16.67         0.92        13.25        13.02        37.22        17.85 
TCGA-VQ-A8PY TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZA-A8F6 
       14.33         9.73        21.04        43.66        38.93        17.26 

$`DEL PEAK  6(2Q32.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT 
       24.00         4.70        19.99        22.82        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        0.23        20.15        25.78        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        33.27        35.21        20.78         2.63 
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-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO 
       26.33        32.61        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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50         2.66        12.92        13.48        13.22         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW 
        5.49        21.37         8.71        13.41        83.24        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       10.85        10.36         5.92        10.45        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.33        13.38        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       25.25        12.00        12.03        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         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        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       53.95         9.30        15.78        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
        5.29         3.42        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        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        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       14.37         3.42         2.10         1.32         2.66        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        2.66        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       27.12         9.34        28.14         6.28        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       31.96         9.86        20.88        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        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 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 
        7.17        12.33        12.30        12.39        12.59        15.39 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        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-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         1.02         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
       19.96         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 
        6.21        77.29        52.21        30.51         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.80        21.17        14.07        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39        12.46        13.35        19.53         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X 
        6.74        12.59         6.51        10.62        11.70        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        37.64         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 
       16.87        19.04         5.79        48.79         5.46        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       43.36        21.73        37.41        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       34.29        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-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 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
        4.54         6.58         5.72        66.81         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        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43         0.79 

  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                          0.0                           0.1 
  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 
                        14.04                         13.87 
[1] "0.0 - 68.0 (14.0)"  "0.1 - 122.3 (13.9)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(2Q32.1) MUTATED         2        1        9        4        13
  DEL PEAK  6(2Q32.1) WILD-TYPE       8       20       38       29        74
                               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        76        25         81         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         37       44         4
D44V3, multiclass
            clus
vv           DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             1                            20
  STAGE IB                             9                            38
  STAGE II                             4                            29
  STAGE IIA                           13                            74
  STAGE IIB                           11                            76
  STAGE III                            3                            25
  STAGE IIIA                          14                            81
  STAGE IIIB                          10                            62
  STAGE IIIC                           9                            37
  STAGE IV                             5                            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  6(2Q32.1) MUTATED       4  19  41  19
  DEL PEAK  6(2Q32.1) WILD-TYPE    51 117 242 105
D44V4, multiclass
       clus
vv      DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  T0+T1                           4                            51
  T2                             19                           117
  T3                             41                           242
  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    33  19  12  18
  DEL PEAK  6(2Q32.1) WILD-TYPE 174 168  86  78
D44V5, multiclass
    clus
vv   DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  N0                          33                           174
  N1                          19                           168
  N2                          12                            86
  N3                          18                            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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    76   3
  DEL PEAK  6(2Q32.1) WILD-TYPE 448  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     76    3
  DEL PEAK  6(2Q32.1) WILD-TYPE  448   36
   clus
vv  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  0                          76                           448
  1                           3                            36
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    26  61
  DEL PEAK  6(2Q32.1) WILD-TYPE 159 379
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     26   61
  DEL PEAK  6(2Q32.1) WILD-TYPE  159  379
        clus
vv       DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  FEMALE                          26                           159
  MALE                            61                           379
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    62  15
  DEL PEAK  6(2Q32.1) WILD-TYPE 383 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     62   15
  DEL PEAK  6(2Q32.1) WILD-TYPE  383  104
     clus
vv    DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  NO                           62                           383
  YES                          15                           104
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(2Q32.1) MUTATED      19                         2
  DEL PEAK  6(2Q32.1) WILD-TYPE   115                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(2Q32.1) MUTATED                                           0    57
  DEL PEAK  6(2Q32.1) WILD-TYPE                                         1   335
D44V11, multiclass
                                           clus
vv                                          DEL PEAK  6(2Q32.1) MUTATED
  ASIAN                                                              19
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              57
                                           clus
vv                                          DEL PEAK  6(2Q32.1) WILD-TYPE
  ASIAN                                                               115
  BLACK OR AFRICAN AMERICAN                                            15
  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"
D44V12, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED     0  56
  DEL PEAK  6(2Q32.1) WILD-TYPE  11 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED      0   56
  DEL PEAK  6(2Q32.1) WILD-TYPE   11  348
                        clus
vv                       DEL PEAK  6(2Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       DEL PEAK  6(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           348
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK  7(2Q33.3) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(2Q33.3) MUTATED    51  31
  DEL PEAK  7(2Q33.3) WILD-TYPE 303 214
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           82                           517 
  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                           31                           214 
$`DEL PEAK  7(2Q33.3) MUTATED`
TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
       20.02        27.35        26.93        35.21         0.85         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A43H 
       20.12        18.64         0.79        68.02        25.22         0.30 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN 
       58.59        15.48         3.02        16.47        13.55         5.49 
TCGA-LN-A49K TCGA-LN-A49V TCGA-LN-A4MQ TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ 
        5.92        12.59        12.33        10.52        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A8W8 TCGA-R6-A8WC 
       12.33        13.38        12.26         8.02         2.89         2.30 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-XP-A8T6 TCGA-Z6-A9VB 
       25.81        27.09        12.43        52.27        25.08         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7901 
        2.66        19.73        19.33         9.17        12.16         3.45 
TCGA-BR-8058 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8369 TCGA-BR-8687 TCGA-CD-8525 
       37.25         9.60        29.42        14.04         8.22        12.59 
TCGA-CD-8526 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4300 TCGA-CG-4462 
       12.53        12.07        12.82         6.31        20.02         0.00 
TCGA-CG-5720 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 
        0.99        12.03        12.66        20.91        17.19        15.22 
TCGA-D7-8573 TCGA-D7-8576 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4G8 
       19.50        14.66        63.06        26.47         5.92        22.68 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4HD TCGA-IN-A6RI 
       22.75        25.81         6.58         2.10        33.40        18.38 
TCGA-IN-AB1V TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PC TCGA-VQ-A8PK 
       15.75         5.46        13.25        13.02        46.26        17.85 
TCGA-VQ-A8PY TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6J 
       14.33        43.66        38.93        27.55 

$`DEL PEAK  7(2Q33.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
       27.12         5.16        47.05        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GH 
       16.24         0.23        20.15         9.86        25.78        31.27 
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-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YA 
       16.24         4.21        32.45         7.69        33.27        20.78 
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-A97H TCGA-IG-A97I TCGA-JY-A6F8 
        9.96        14.86         4.67        14.50        12.16       122.10 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C 
       44.75         3.68        41.52        47.38        21.70        23.18 
TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF 
       31.56        24.03         6.28         3.16        30.25        26.33 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        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-A4OX 
        1.38         3.16         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        2.60        25.12         7.40         3.75        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        13.48        13.22         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.41        83.24        52.57        46.09        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        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        12.85        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-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.03        13.18         0.13        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         7.59         5.06        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35        53.95         9.30        15.78        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
       20.38         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        8.98        22.82         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 
       33.70        18.18        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        18.21        41.23        14.37         3.42         2.10 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       58.03        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.44         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       33.21        14.43        11.44         0.69        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58         9.86        20.88        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       28.34         0.66        32.52        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.76         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       11.64        15.39        12.43        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       11.61         6.58        12.20        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        19.07        12.03         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-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-6518 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-D7-6818 TCGA-D7-6820 
       13.35        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       12.33        24.72        16.80        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        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       22.29        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
        5.03        13.58         0.56         5.52         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       52.21        30.51         1.51        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        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        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        13.51         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       36.95         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-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 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        16.31        22.19         2.50        12.79 
TCGA-VQ-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 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        2.66        42.54        11.24        18.41        28.41        32.94 
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        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE 
                          0.0                           0.1 
  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 
                       13.465                        14.010 
[1] "0.0 - 68.0 (13.5)"  "0.1 - 122.3 (14.0)"
[1] "hr=" "1"  
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(2Q33.3) MUTATED         2        2        7        2        15
  DEL PEAK  7(2Q33.3) WILD-TYPE       8       19       40       31        72
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(2Q33.3) MUTATED          11         5         17          9
  DEL PEAK  7(2Q33.3) WILD-TYPE        76        23         78         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  7(2Q33.3) MUTATED            8        4         0
  DEL PEAK  7(2Q33.3) WILD-TYPE         38       45         4
D45V3, multiclass
            clus
vv           DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             2                            19
  STAGE IB                             7                            40
  STAGE II                             2                            31
  STAGE IIA                           15                            72
  STAGE IIB                           11                            76
  STAGE III                            5                            23
  STAGE IIIA                          17                            78
  STAGE IIIB                           9                            63
  STAGE IIIC                           8                            38
  STAGE IV                             4                            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  7(2Q33.3) MUTATED       4  16  47  15
  DEL PEAK  7(2Q33.3) WILD-TYPE    51 120 236 109
D45V4, multiclass
       clus
vv      DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  T0+T1                           4                            51
  T2                             16                           120
  T3                             47                           236
  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    31  25  11  15
  DEL PEAK  7(2Q33.3) WILD-TYPE 176 162  87  81
D45V5, multiclass
    clus
vv   DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  N0                          31                           176
  N1                          25                           162
  N2                          11                            87
  N3                          15                            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"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED    74   3
  DEL PEAK  7(2Q33.3) WILD-TYPE 450  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED     74    3
  DEL PEAK  7(2Q33.3) WILD-TYPE  450   36
   clus
vv  DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  0                          74                           450
  1                           3                            36
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED    23  62
  DEL PEAK  7(2Q33.3) WILD-TYPE 162 378
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED     23   62
  DEL PEAK  7(2Q33.3) WILD-TYPE  162  378
        clus
vv       DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  FEMALE                          23                           162
  MALE                            62                           378
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED    60  18
  DEL PEAK  7(2Q33.3) WILD-TYPE 385 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED     60   18
  DEL PEAK  7(2Q33.3) WILD-TYPE  385  101
     clus
vv    DEL PEAK  7(2Q33.3) MUTATED DEL PEAK  7(2Q33.3) WILD-TYPE
  NO                           60                           385
  YES                          18                           101
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(2Q33.3) MUTATED      23                         3
  DEL PEAK  7(2Q33.3) WILD-TYPE   111                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  7(2Q33.3) MUTATED                                           0    51
  DEL PEAK  7(2Q33.3) WILD-TYPE                                         1   341
D45V11, multiclass
                                           clus
vv                                          DEL PEAK  7(2Q33.3) MUTATED
  ASIAN                                                              23
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              51
                                           clus
vv                                          DEL PEAK  7(2Q33.3) WILD-TYPE
  ASIAN                                                               111
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               341
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  7(2Q33.3) MUTATED     1  53
  DEL PEAK  7(2Q33.3) WILD-TYPE  10 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(2Q33.3) MUTATED      1   53
  DEL PEAK  7(2Q33.3) WILD-TYPE   10  351
                        clus
vv                       DEL PEAK  7(2Q33.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       DEL PEAK  7(2Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           351
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK  8(2Q37.2) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(2Q37.2) MUTATED    75  44
  DEL PEAK  8(2Q37.2) WILD-TYPE 279 201
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          119                           480 
  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                           44                           201 
$`DEL PEAK  8(2Q37.2) MUTATED`
TCGA-L5-A8NT TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GM 
       27.12        20.02        27.35        26.93        25.78        13.94 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A5B8 
       35.21         0.85         2.63        20.12        18.64         0.79 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-L5-A43H TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88S 
       14.50        68.02         0.30         3.16        58.59        15.48 
TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49K TCGA-LN-A49L 
        3.02        16.47        13.55        13.22         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4MQ 
       12.66        12.59        13.25        12.59        12.59        12.33 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       10.52        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FQ TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX 
       12.85         2.30         7.00        20.38        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
       25.81        27.09        12.43        28.11        18.18        52.27 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-6565 TCGA-BR-6709 
        3.42         1.32         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        37.25        14.43        11.44         9.60 
TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8485 
       29.42        31.10        14.79         7.36        25.18         9.21 
TCGA-BR-8677 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8526 
       26.73         8.22        20.65        13.15        12.59        12.53 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 
       15.39        12.07        12.82         6.31        11.31        20.02 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5719 
        8.05        14.01        19.07        18.97        12.00         1.02 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       12.66        20.55        17.19        15.22        15.98        12.36 
TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 
       14.66        11.24        22.29        52.21        26.47         5.92 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RR TCGA-IN-AB1V 
       22.75         8.98        12.95        33.40         6.74        15.75 
TCGA-R5-A7ZE TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A8PX TCGA-VQ-A8PY 
       18.21        13.25        13.02        22.19        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        32.88         9.04         4.54         5.72 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
       18.41        43.66        38.93        54.12        16.14 

$`DEL PEAK  8(2Q37.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
        0.23        20.15         9.86        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        7.69        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-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25        26.33        32.61        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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50         2.66        12.92        13.48         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       21.37         8.71        13.41        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85        10.36        12.43        13.41        12.33        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        15.35        12.62        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        12.85        15.52        11.54        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.33        25.25        12.00        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       15.78         2.89        12.69         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY 
        9.27        22.82         1.55        18.31         8.12        33.70 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-5816 
       25.08        41.23        14.37         2.10        58.03        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-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        36.16        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 
       15.32        28.73         9.07        29.56        33.21         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       29.59        32.25         8.05         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
        3.32        11.80        31.27        25.05         3.72         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.76         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       12.59        11.64        12.43        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        6.58        12.20        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       15.95         1.02         7.99        54.08         4.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       12.03         0.00         9.01         7.07        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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        20.91        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        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.31        11.44        20.32 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-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-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       30.51         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        29.00        23.84        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       37.64        36.95         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       12.79         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        13.35        29.59        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       21.83        61.22         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.73        55.56         2.01        55.43         6.58        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B 
       21.04         2.66        42.54        11.24        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        26.04        27.55        12.43        17.26         0.79 

  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE 
                          0.3                           0.0 
  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 
                        13.55                         14.04 
[1] "0.3 - 68.0 (13.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(2Q37.2) MUTATED         1        5        9        7        20
  DEL PEAK  8(2Q37.2) WILD-TYPE       9       16       38       26        67
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(2Q37.2) MUTATED          17        10         20         12
  DEL PEAK  8(2Q37.2) WILD-TYPE        70        18         75         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  8(2Q37.2) MUTATED           10        7         1
  DEL PEAK  8(2Q37.2) WILD-TYPE         36       42         3
D46V3, multiclass
            clus
vv           DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             5                            16
  STAGE IB                             9                            38
  STAGE II                             7                            26
  STAGE IIA                           20                            67
  STAGE IIB                           17                            70
  STAGE III                           10                            18
  STAGE IIIA                          20                            75
  STAGE IIIB                          12                            60
  STAGE IIIC                          10                            36
  STAGE IV                             7                            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  8(2Q37.2) MUTATED       9  26  61  24
  DEL PEAK  8(2Q37.2) WILD-TYPE    46 110 222 100
D46V4, multiclass
       clus
vv      DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  T0+T1                           9                            46
  T2                             26                           110
  T3                             61                           222
  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    46  38  16  19
  DEL PEAK  8(2Q37.2) WILD-TYPE 161 149  82  77
D46V5, multiclass
    clus
vv   DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  N0                          46                           161
  N1                          38                           149
  N2                          16                            82
  N3                          19                            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"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED   109   3
  DEL PEAK  8(2Q37.2) WILD-TYPE 415  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED    109    3
  DEL PEAK  8(2Q37.2) WILD-TYPE  415   36
   clus
vv  DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  0                         109                           415
  1                           3                            36
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED    37  85
  DEL PEAK  8(2Q37.2) WILD-TYPE 148 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED     37   85
  DEL PEAK  8(2Q37.2) WILD-TYPE  148  355
        clus
vv       DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  FEMALE                          37                           148
  MALE                            85                           355
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED    85  28
  DEL PEAK  8(2Q37.2) WILD-TYPE 360  91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED     85   28
  DEL PEAK  8(2Q37.2) WILD-TYPE  360   91
     clus
vv    DEL PEAK  8(2Q37.2) MUTATED DEL PEAK  8(2Q37.2) WILD-TYPE
  NO                           85                           360
  YES                          28                            91
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(2Q37.2) MUTATED      31                         3
  DEL PEAK  8(2Q37.2) WILD-TYPE   103                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(2Q37.2) MUTATED                                           0    70
  DEL PEAK  8(2Q37.2) WILD-TYPE                                         1   322
D46V11, multiclass
                                           clus
vv                                          DEL PEAK  8(2Q37.2) MUTATED
  ASIAN                                                              31
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              70
                                           clus
vv                                          DEL PEAK  8(2Q37.2) WILD-TYPE
  ASIAN                                                               103
  BLACK OR AFRICAN AMERICAN                                            14
  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"
D46V12, binary
                               cls
clus                              0   1
  DEL PEAK  8(2Q37.2) MUTATED     0  75
  DEL PEAK  8(2Q37.2) WILD-TYPE  11 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(2Q37.2) MUTATED      0   75
  DEL PEAK  8(2Q37.2) WILD-TYPE   11  329
                        clus
vv                       DEL PEAK  8(2Q37.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK  8(2Q37.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           329
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK  9(3P26.2) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P26.2) MUTATED   151  92
  DEL PEAK  9(3P26.2) WILD-TYPE 203 153
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                          243                           356 
  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                           92                           153 
$`DEL PEAK  9(3P26.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A8NG TCGA-S8-A6BV 
       60.39         4.31         8.94         4.70        35.97        20.02 
TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GL 
       47.05         9.86        27.35        26.93        14.30         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 
       13.94         8.94        16.24         4.21         7.69        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS 
       35.21         0.85        20.78         2.63        20.12         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        0.53        17.03         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM 
       12.16        68.02        30.25         0.30        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-A8NH 
       15.48         2.60         7.40        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
       16.47        13.55         5.49        52.57        10.85         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.62        12.46        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 
       12.85        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-LN-A8HZ 
       25.25        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A8W8 
       33.11         7.82         7.59         7.04        38.40         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EO 
       12.69         7.00        20.38         3.42         9.27        25.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ 
       27.09        12.43        18.31         8.12        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 
        1.32        11.01         9.44         6.61        18.35         4.08 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 
       19.33         9.17        25.61        31.20        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 
       39.78         9.07        33.21        37.25         0.69         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       19.96         7.40        13.08         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       20.22        24.79        31.96        20.88         8.22        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 
        7.53        34.98         1.48        12.89         0.72         0.53 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       13.51        20.65        20.42         1.15        21.44        13.02 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A487 
       13.18        12.10        12.53         7.17        15.39        12.30 
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-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 
       12.03        18.97        36.00        15.02         4.01        12.66 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-A6EX 
       18.54        13.35        17.19        15.22        12.79        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-7916 
       20.32        15.65         0.62         7.99        19.53        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8245 TCGA-HU-8249 
       17.06         0.56         5.52         6.21        18.15        28.96 
TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
       24.26         3.25        22.75         6.58         2.10        23.84 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       23.80        36.36        18.38         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
       10.62         5.56        63.62        37.64        36.95        14.04 
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-A8PY 
        7.73        22.19        12.79         2.70        17.85        14.33 
TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A925 
       39.45        42.64         9.50         9.73         2.01         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       21.04        42.54        18.41        38.93        32.94        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`DEL PEAK  9(3P26.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28        24.00        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        0.36        27.12         5.16        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ 
       16.24         0.23        20.15        25.78        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GR TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP 
        7.63        32.45        18.64         9.30        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67       122.10        44.75         3.68        41.52        47.38 
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-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OU 
        3.16        26.33        21.01        18.35         1.38        29.00 
TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NI TCGA-L5-A8NL 
        7.43        25.12         3.75         3.02        13.48        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-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       10.36        10.45        12.66        12.59        13.25        12.59 
TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ 
       11.54        12.03         8.02         5.06        16.31         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RE 
       53.95         9.30        15.78         2.30         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-Z6-AAPN 
       15.35         8.98        22.82         1.55        28.11         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       19.73        58.03        26.70        11.70        19.56         9.47 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        6.97         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       18.05        19.89        12.16         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       44.94        21.90         9.21        36.16        35.84        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
       15.32        28.73         3.45        29.56        14.43        11.44 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        2.20        15.58         6.18        31.10         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A44U 
        7.53        26.73        32.58         9.86        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.66        32.52         0.46        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 
       13.15        13.35        11.21        12.76        12.59        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.20        11.77        12.62        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        19.07         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        0.99       105.07        12.03        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 
       18.84        18.61        17.85        10.26        15.98        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        22.29         8.38         4.34        19.96         7.13 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 
       14.47        72.23        21.27        11.38         3.48        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       59.54         5.03        13.58        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       30.51        26.47         1.51         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26        12.95        29.00 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NU 
        3.39        12.46        13.35        19.53         6.74        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI 
       15.75        13.51         2.53         3.72        19.73        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       19.04        48.79        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E 
       13.35        29.59        64.57        73.41        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       61.22        18.74        20.81        32.88         1.71        60.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       55.56         9.04        55.43         6.58         5.72        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        11.24        43.66        28.41        17.13        26.04 
TCGA-VQ-AA6I TCGA-ZA-A8F6 
       16.14        17.26 

  DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE 
                         0.13                          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 
                       12.920                        15.665 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1"  
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P26.2) MUTATED         5        7       16        9        43
  DEL PEAK  9(3P26.2) WILD-TYPE       5       14       31       24        44
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P26.2) MUTATED          36        15         39         25
  DEL PEAK  9(3P26.2) WILD-TYPE        51        13         56         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK  9(3P26.2) MUTATED           17       18         2
  DEL PEAK  9(3P26.2) WILD-TYPE         29       31         2
D47V3, multiclass
            clus
vv           DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  STAGE I                              5                             5
  STAGE IA                             7                            14
  STAGE IB                            16                            31
  STAGE II                             9                            24
  STAGE IIA                           43                            44
  STAGE IIB                           36                            51
  STAGE III                           15                            13
  STAGE IIIA                          39                            56
  STAGE IIIB                          25                            47
  STAGE IIIC                          17                            29
  STAGE IV                            18                            31
  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      26  53 116  44
  DEL PEAK  9(3P26.2) WILD-TYPE    29  83 167  80
D47V4, multiclass
       clus
vv      DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  T0+T1                          26                            29
  T2                             53                            83
  T3                            116                           167
  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    82  80  42  31
  DEL PEAK  9(3P26.2) WILD-TYPE 125 107  56  65
D47V5, multiclass
    clus
vv   DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  N0                          82                           125
  N1                          80                           107
  N2                          42                            56
  N3                          31                            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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED   206  18
  DEL PEAK  9(3P26.2) WILD-TYPE 318  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED    206   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                         206                           318
  1                          18                            21
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED    64 186
  DEL PEAK  9(3P26.2) WILD-TYPE 121 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED     64  186
  DEL PEAK  9(3P26.2) WILD-TYPE  121  254
        clus
vv       DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  FEMALE                          64                           121
  MALE                           186                           254
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED   177  52
  DEL PEAK  9(3P26.2) WILD-TYPE 268  67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED    177   52
  DEL PEAK  9(3P26.2) WILD-TYPE  268   67
     clus
vv    DEL PEAK  9(3P26.2) MUTATED DEL PEAK  9(3P26.2) WILD-TYPE
  NO                          177                           268
  YES                          52                            67
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(3P26.2) MUTATED      60                         7
  DEL PEAK  9(3P26.2) WILD-TYPE    74                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(3P26.2) MUTATED                                           1   153
  DEL PEAK  9(3P26.2) WILD-TYPE                                         0   239
D47V11, multiclass
                                           clus
vv                                          DEL PEAK  9(3P26.2) MUTATED
  ASIAN                                                              60
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             153
                                           clus
vv                                          DEL PEAK  9(3P26.2) WILD-TYPE
  ASIAN                                                                74
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               239
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P26.2) MUTATED     5 156
  DEL PEAK  9(3P26.2) WILD-TYPE   6 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P26.2) MUTATED      5  156
  DEL PEAK  9(3P26.2) WILD-TYPE    6  248
                        clus
vv                       DEL PEAK  9(3P26.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         156
                        clus
vv                       DEL PEAK  9(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 10(3P14.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3P14.2) MUTATED   164 113
  DEL PEAK 10(3P14.2) WILD-TYPE 190 132
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          277                           322 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          113                           132 
$`DEL PEAK 10(3P14.2) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A94U 
       35.97         5.16        20.02        47.05         9.86        26.93 
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        35.21         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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       68.02        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OW TCGA-L5-A4OX 
       47.93         3.32         7.17         1.38         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
       15.48         2.60         7.40         2.66        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G 
       13.55         5.49         8.71        13.41        52.57        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       13.15        15.35        13.25        12.62        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        12.85        15.52 
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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L6 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
        8.02         7.59         7.04         2.89        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         3.42        16.44         9.27        25.81        27.09 
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        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.21        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 
        1.32         2.66        26.70        19.56        11.01         6.61 
TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6803 
        4.08        17.29        19.33         9.17        25.61        31.20 
TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 
       44.94        35.24        33.63        39.78        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 
        9.07        33.21        37.25        11.44         0.69         2.66 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 
        5.39        25.18         9.21        20.22        20.88         8.22 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       13.87         7.53        34.98         1.48        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        0.53        13.51        20.65         1.15        21.44        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 
       13.15        13.18        12.10        12.76        12.53         7.17 
TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4436 
       15.39        12.30        20.02         3.02        15.95         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 
        8.05        54.08         4.01        14.01        12.03        18.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5577 
       36.00         1.02        12.03        15.02         4.01        25.71 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.54        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6EX 
       15.22        12.79        12.33        14.27        13.78        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
       11.44        20.32        19.96         0.62         7.99        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HJ-7597 
       14.07        17.06         0.56         5.52         6.21        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G6 
        5.92        18.15        28.96        22.32        22.82        24.26 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-A6RI 
        6.58         2.10        23.84        14.07        36.36        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 
       13.51         5.56        63.62        37.64        36.95        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
       18.21         8.52        74.53        16.67        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        5.79         5.46        13.25        37.41         7.73        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N 
        2.70        17.85         9.27        13.35        14.33        18.74 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       42.64         9.50         9.04         2.01        55.43         4.54 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        38.93        32.94        54.12        26.04        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 10(3P14.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        60.39        34.85        19.99        22.82        27.12 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-IG-A4QT 
       27.35        25.78        31.27        58.55         7.63         9.30 
TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       12.82        14.86         4.67       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        6.28         3.16        18.35         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI 
       29.00        25.12         3.75         3.02        55.50        13.48 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.22         7.76        21.37        83.24        46.09        10.36 
TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A4A9 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6L4 
       13.38        12.59        11.54         7.82         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
       38.40         6.35        53.95         9.30        15.78         2.30 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-ZR-A9CJ 
        5.29        15.35         8.98        22.82         1.55        19.73 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       58.03        11.70         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        26.10        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7197 
       12.16         8.98        40.21        30.90        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8059 
       36.16        35.84        18.15        28.73        29.56        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       19.96         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       31.96        32.58         9.86        10.68        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       32.52         0.46        20.42        16.14         5.13        13.41 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       13.35        11.21        12.59        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
       12.62        27.02         1.02        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
        9.01         7.07        12.00        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
        6.02         0.99       105.07        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        12.66        20.91        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       17.85        15.98        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       16.44         5.92        36.43        14.76        26.43        11.24 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 
       22.29        15.65         8.38         4.34         7.13        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-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.03        13.58        77.29        63.06        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
        1.51        24.39        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
       22.68        24.20        21.37        29.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        0.26        12.95        29.00        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       33.40         3.45        18.81         3.39        12.46        19.53 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       11.70        15.75         2.53         3.72        19.73        14.04 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-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-A8DZ 
       35.61        16.87        19.04         0.92        48.79        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       18.48        43.36        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       34.29        46.26        16.31         2.50        12.79         1.87 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        29.59        64.57        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U 
       11.70        21.83        61.22        20.81        32.88         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
       60.85         9.73        55.56         6.58         5.72        66.81 
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        43.66        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        16.14        27.55        17.26 

  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                          0.1                           0.0 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                        74.53                        122.30 
  DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE 
                        13.15                         16.06 
[1] "0.1 - 74.5 (13.2)"  "0.0 - 122.3 (16.1)"
[1] "hr=" "1.3"
D48V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3P14.2) MUTATED         5        7       16       14        52
  DEL PEAK 10(3P14.2) WILD-TYPE       5       14       31       19        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3P14.2) MUTATED          44        17         47         24
  DEL PEAK 10(3P14.2) WILD-TYPE        43        11         48         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 10(3P14.2) MUTATED           16       21         3
  DEL PEAK 10(3P14.2) WILD-TYPE         30       28         1
D48V3, multiclass
            clus
vv           DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  STAGE I                              5                             5
  STAGE IA                             7                            14
  STAGE IB                            16                            31
  STAGE II                            14                            19
  STAGE IIA                           52                            35
  STAGE IIB                           44                            43
  STAGE III                           17                            11
  STAGE IIIA                          47                            48
  STAGE IIIB                          24                            48
  STAGE IIIC                          16                            30
  STAGE IV                            21                            28
  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      31  64 133  45
  DEL PEAK 10(3P14.2) WILD-TYPE    24  72 150  79
D48V4, multiclass
       clus
vv      DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  T0+T1                          31                            24
  T2                             64                            72
  T3                            133                           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 10(3P14.2) MUTATED    99  96  44  32
  DEL PEAK 10(3P14.2) WILD-TYPE 108  91  54  64
D48V5, multiclass
    clus
vv   DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  N0                          99                           108
  N1                          96                            91
  N2                          44                            54
  N3                          32                            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"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED   232  21
  DEL PEAK 10(3P14.2) WILD-TYPE 292  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED    232   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                         232                           292
  1                          21                            18
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED    79 203
  DEL PEAK 10(3P14.2) WILD-TYPE 106 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED     79  203
  DEL PEAK 10(3P14.2) WILD-TYPE  106  237
        clus
vv       DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  FEMALE                          79                           106
  MALE                           203                           237
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED   203  56
  DEL PEAK 10(3P14.2) WILD-TYPE 242  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED    203   56
  DEL PEAK 10(3P14.2) WILD-TYPE  242   63
     clus
vv    DEL PEAK 10(3P14.2) MUTATED DEL PEAK 10(3P14.2) WILD-TYPE
  NO                          203                           242
  YES                          56                            63
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(3P14.2) MUTATED      73                         5
  DEL PEAK 10(3P14.2) WILD-TYPE    61                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(3P14.2) MUTATED                                           0   165
  DEL PEAK 10(3P14.2) WILD-TYPE                                         1   227
D48V11, multiclass
                                           clus
vv                                          DEL PEAK 10(3P14.2) MUTATED
  ASIAN                                                              73
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             165
                                           clus
vv                                          DEL PEAK 10(3P14.2) WILD-TYPE
  ASIAN                                                                61
  BLACK OR AFRICAN AMERICAN                                            12
  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"
D48V12, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P14.2) MUTATED     6 176
  DEL PEAK 10(3P14.2) WILD-TYPE   5 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P14.2) MUTATED      6  176
  DEL PEAK 10(3P14.2) WILD-TYPE    5  228
                        clus
vv                       DEL PEAK 10(3P14.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         176
                        clus
vv                       DEL PEAK 10(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           228
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 11(3Q11.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(3Q11.1) MUTATED    55  40
  DEL PEAK 11(3Q11.1) WILD-TYPE 299 205
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           95                           504 
  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                           40                           205 
$`DEL PEAK 11(3Q11.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A88Y TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GM 
       34.85         0.36         9.86        26.93        14.30        13.94 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A5S3 
        4.21        32.45         7.69         2.63        20.12        23.41 
TCGA-JY-A6FD TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OX 
       68.02        30.25         0.30        32.61         3.32         7.43 
TCGA-L5-A8NH TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A6 TCGA-LN-A5U5 
       12.92        10.45        13.38        12.46        12.85         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-R6-A8W8 
       12.33        12.23        12.03        13.18        13.38         2.89 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-BR-4255 
       12.69         7.00         9.27        46.19        18.21         4.08 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       17.29        19.33         9.17        35.24        33.63        39.78 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8485 
       33.21        11.44         0.69         2.66         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       20.22        20.88         7.53        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8533 
        0.72        13.51         1.15        21.44        13.15        15.39 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-5724 
       20.02        54.08        14.01        12.03        18.97        12.03 
TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-FP-8099 
       12.66        20.55        15.22        11.31         0.62        17.06 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-IN-7806 
        0.56         5.52        28.96         3.25         6.58        36.36 
TCGA-IN-A6RL TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7ZF 
       13.35         2.53         5.56        37.64        36.95         8.52 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A91N TCGA-VQ-A91X 
        5.79        13.25         7.73         2.70        18.74         9.50 
TCGA-VQ-A91Y TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6D 
        9.73        21.04        42.54        32.94        17.13 

$`DEL PEAK 11(3Q11.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ 
        0.23        20.15        27.35        25.78        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL 
        7.63         5.92         8.94        16.24        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
        0.85        20.78        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-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16       122.10        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       47.38        21.70        23.18        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        6.28         3.16        26.33        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        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-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       12.59        13.25        12.62        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-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       25.25        10.52        12.00        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       12.03        12.85        12.26        33.11         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        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB 
       53.95         9.30        15.78         2.30        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        3.42        16.44        15.35         8.98        25.81        27.09 
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 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        1.32         2.66        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       31.27        14.79         7.36        25.05         3.72        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        10.68        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.31        12.30        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        1.02         7.99         8.05         4.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85        13.35        17.19        10.26        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-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-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 
       22.29        59.54         5.03        13.58         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD 
       24.30         5.59        24.26        22.68        24.20        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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38        12.46        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       15.75        13.51        63.62         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.02        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
        2.50        12.79        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
        1.71        42.64        60.85        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6F 
       11.24        18.41        43.66        28.41        38.93        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        27.55        12.43        17.26         0.79 

  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE 
                          0.3                           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 
                        12.89                         14.45 
[1] "0.3 - 68.0 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D49V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(3Q11.1) MUTATED         2        2        3        6        12
  DEL PEAK 11(3Q11.1) WILD-TYPE       8       19       44       27        75
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(3Q11.1) MUTATED          18         5         18          9
  DEL PEAK 11(3Q11.1) WILD-TYPE        69        23         77         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 11(3Q11.1) MUTATED            6        9         0
  DEL PEAK 11(3Q11.1) WILD-TYPE         40       40         4
D49V3, multiclass
            clus
vv           DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             2                            19
  STAGE IB                             3                            44
  STAGE II                             6                            27
  STAGE IIA                           12                            75
  STAGE IIB                           18                            69
  STAGE III                            5                            23
  STAGE IIIA                          18                            77
  STAGE IIIB                           9                            63
  STAGE IIIC                           6                            40
  STAGE IV                             9                            40
  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  16  43  24
  DEL PEAK 11(3Q11.1) WILD-TYPE    44 120 240 100
D49V4, multiclass
       clus
vv      DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  T0+T1                          11                            44
  T2                             16                           120
  T3                             43                           240
  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    30  34  19  11
  DEL PEAK 11(3Q11.1) WILD-TYPE 177 153  79  85
D49V5, multiclass
    clus
vv   DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  N0                          30                           177
  N1                          34                           153
  N2                          19                            79
  N3                          11                            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"
D49V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED    83   7
  DEL PEAK 11(3Q11.1) WILD-TYPE 441  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED     83    7
  DEL PEAK 11(3Q11.1) WILD-TYPE  441   32
   clus
vv  DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  0                          83                           441
  1                           7                            32
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED    25  73
  DEL PEAK 11(3Q11.1) WILD-TYPE 160 367
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED     25   73
  DEL PEAK 11(3Q11.1) WILD-TYPE  160  367
        clus
vv       DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  FEMALE                          25                           160
  MALE                            73                           367
[1] 2 2
[1] FALSE
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED    72  15
  DEL PEAK 11(3Q11.1) WILD-TYPE 373 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED     72   15
  DEL PEAK 11(3Q11.1) WILD-TYPE  373  104
     clus
vv    DEL PEAK 11(3Q11.1) MUTATED DEL PEAK 11(3Q11.1) WILD-TYPE
  NO                           72                           373
  YES                          15                           104
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(3Q11.1) MUTATED      22                         2
  DEL PEAK 11(3Q11.1) WILD-TYPE   112                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(3Q11.1) MUTATED                                           0    60
  DEL PEAK 11(3Q11.1) WILD-TYPE                                         1   332
D49V11, multiclass
                                           clus
vv                                          DEL PEAK 11(3Q11.1) MUTATED
  ASIAN                                                              22
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              60
                                           clus
vv                                          DEL PEAK 11(3Q11.1) WILD-TYPE
  ASIAN                                                               112
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               332
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 11(3Q11.1) MUTATED     1  63
  DEL PEAK 11(3Q11.1) WILD-TYPE  10 341
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(3Q11.1) MUTATED      1   63
  DEL PEAK 11(3Q11.1) WILD-TYPE   10  341
                        clus
vv                       DEL PEAK 11(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK 11(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           341
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 12(3Q26.31) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(3Q26.31) MUTATED    35  26
  DEL PEAK 12(3Q26.31) WILD-TYPE 319 219
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            61                            538 
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                            26                            219 
$`DEL PEAK 12(3Q26.31) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       34.85        18.28         9.86        26.93        25.78        14.30 
TCGA-2H-A9GM TCGA-IC-A6RE TCGA-JY-A93D TCGA-L5-A4OH TCGA-L5-A4OX TCGA-L5-A891 
       13.94         7.69        31.56        32.61         7.43         3.75 
TCGA-L5-A8NH TCGA-L5-A8NW TCGA-R6-A6DN TCGA-RE-A7BO TCGA-VR-A8EU TCGA-X8-AAAR 
       12.92        46.09         8.02         7.00        18.31        18.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8485 TCGA-BR-8486 
       35.24        33.63        33.21         0.69         9.21        20.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
       10.68        13.87        12.89         0.72        13.51         1.15 
TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4466 TCGA-D7-5578 
       15.39        12.30        54.08        14.01        18.97        12.66 
TCGA-D7-6526 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 
       17.19        12.33        19.50        11.31        11.44        22.29 
TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4GU TCGA-IN-7806 
        7.99         5.52        28.96        25.81         6.58        36.36 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7ZF TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8DV 
        5.56        37.64         8.52        16.67         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A94O TCGA-VQ-A94R 
       43.36        22.19        42.64         9.50        21.04        42.54 
TCGA-VQ-AA6B 
       32.94 

$`DEL PEAK 12(3Q26.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39         4.31         8.94        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.23        20.15        27.35        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
        5.92         8.94        16.24         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         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-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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
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-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.13        15.48         2.60        25.12         7.40 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK 
        3.02        55.50         2.66        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-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        52.57        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        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        12.85        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-A8HZ 
       10.52        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.38        13.18         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       15.35         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43         1.55         8.12        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       52.27        46.19        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       25.08        41.23        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.66        19.73        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.01         9.47         9.44         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        36.16        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        9.86        20.88         8.22        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.98         1.48        27.55        28.57         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        28.34         0.66        32.52         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        12.07        12.82        12.43         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       11.31        12.43        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        7.99         8.05         4.01        29.98        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       15.22        15.98        12.79        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        20.32        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       19.96         7.13         0.62        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       63.06        52.21        30.51        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         2.53        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
       57.44         8.94        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79        13.02        18.48        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
       18.74        20.81        32.88         1.71        60.85         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        5.72        66.81         2.66        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        38.93        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                          0.69                           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 
                         14.30                          13.73 
[1] "0.7 - 54.1 (14.3)"  "0.0 - 122.3 (13.7)"
[1] "hr=" "1"  
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(3Q26.31) MUTATED         1        1        7        2         4
  DEL PEAK 12(3Q26.31) WILD-TYPE       9       20       40       31        83
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(3Q26.31) MUTATED          12         2         12         10
  DEL PEAK 12(3Q26.31) WILD-TYPE        75        26         83         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 12(3Q26.31) MUTATED            4        4         0
  DEL PEAK 12(3Q26.31) WILD-TYPE         42       45         4
D50V3, multiclass
            clus
vv           DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              1                             20
  STAGE IB                              7                             40
  STAGE II                              2                             31
  STAGE IIA                             4                             83
  STAGE IIB                            12                             75
  STAGE III                             2                             26
  STAGE IIIA                           12                             83
  STAGE IIIB                           10                             62
  STAGE IIIC                            4                             42
  STAGE IV                              4                             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 12(3Q26.31) MUTATED       8  10  33  12
  DEL PEAK 12(3Q26.31) WILD-TYPE    47 126 250 112
D50V4, multiclass
       clus
vv      DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  T0+T1                            8                             47
  T2                              10                            126
  T3                              33                            250
  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    18  20  15   9
  DEL PEAK 12(3Q26.31) WILD-TYPE 189 167  83  87
D50V5, multiclass
    clus
vv   DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  N0                           18                            189
  N1                           20                            167
  N2                           15                             83
  N3                            9                             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"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED    56   3
  DEL PEAK 12(3Q26.31) WILD-TYPE 468  36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED     56    3
  DEL PEAK 12(3Q26.31) WILD-TYPE  468   36
   clus
vv  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  0                           56                            468
  1                            3                             36
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED    17  48
  DEL PEAK 12(3Q26.31) WILD-TYPE 168 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED     17   48
  DEL PEAK 12(3Q26.31) WILD-TYPE  168  392
        clus
vv       DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  FEMALE                           17                            168
  MALE                             48                            392
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED    46  10
  DEL PEAK 12(3Q26.31) WILD-TYPE 399 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED     46   10
  DEL PEAK 12(3Q26.31) WILD-TYPE  399  109
     clus
vv    DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE
  NO                            46                            399
  YES                           10                            109
[1] 2 2
[1] FALSE
D50V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 12(3Q26.31) MUTATED"
clus
  DEL PEAK 12(3Q26.31) MUTATED DEL PEAK 12(3Q26.31) WILD-TYPE 
                             1                             67 
                    TCGA-IG-A3I8                     TCGA-IG-A3QL 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A3Y9                     TCGA-IG-A3YA 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A3YB                     TCGA-IG-A3YC 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A51D                     TCGA-IG-A5S3 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-IG-A7DP                     TCGA-KH-A6WC 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49K                     TCGA-LN-A49L 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49M                     TCGA-LN-A49N 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49O                     TCGA-LN-A49P 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49R                     TCGA-LN-A49S 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49U                     TCGA-LN-A49V 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49W                     TCGA-LN-A49X 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A49Y                     TCGA-LN-A4A1 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A2                     TCGA-LN-A4A3 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A4                     TCGA-LN-A4A5 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A6                     TCGA-LN-A4A8 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4A9                     TCGA-LN-A4MQ 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A4MR                     TCGA-LN-A5U5 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A5U6                     TCGA-LN-A5U7 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HV                     TCGA-LN-A7HW 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HX                     TCGA-LN-A7HY 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-LN-A7HZ                     TCGA-V5-A7RB 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-V5-A7RC                     TCGA-V5-A7RE 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-V5-AASV                     TCGA-V5-AASW 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-V5-AASX                     TCGA-VR-A8EO 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EP                     TCGA-VR-A8EQ 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8ER                     TCGA-VR-A8ET 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EW                     TCGA-VR-A8EX 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8EY                     TCGA-VR-A8EZ 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-A8Q7                     TCGA-VR-AA4D 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-AA4G                     TCGA-VR-AA7B 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-VR-AA7D                     TCGA-VR-AA7I 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-XP-A8T6                     TCGA-XP-A8T7 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-XP-A8T8                     TCGA-Z6-A8JD 
"DEL PEAK 12(3Q26.31) WILD-TYPE" "DEL PEAK 12(3Q26.31) WILD-TYPE" 
                    TCGA-Z6-A8JE 
"DEL PEAK 12(3Q26.31) WILD-TYPE" 
D50V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(3Q26.31) MUTATED       9                         2
  DEL PEAK 12(3Q26.31) WILD-TYPE   125                        15
                                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      45
  DEL PEAK 12(3Q26.31) WILD-TYPE   347
D50V11, multiclass
                                           clus
vv                                          DEL PEAK 12(3Q26.31) MUTATED
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               45
                                           clus
vv                                          DEL PEAK 12(3Q26.31) WILD-TYPE
  ASIAN                                                                125
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                347
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 12(3Q26.31) MUTATED     0  37
  DEL PEAK 12(3Q26.31) WILD-TYPE  11 367
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(3Q26.31) MUTATED      0   37
  DEL PEAK 12(3Q26.31) WILD-TYPE   11  367
                        clus
vv                       DEL PEAK 12(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK 12(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            367
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 13(4P16.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4P16.3) MUTATED   152 110
  DEL PEAK 13(4P16.3) WILD-TYPE 202 135
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          262                           337 
  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                          110                           135 
$`DEL PEAK 13(4P16.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         8.94        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-CG-4444 TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI 
       27.12        47.05         9.86        27.35        26.93        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         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-A3YC 
        7.69        33.27        35.21         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97I 
       18.64         3.88         0.79         9.96         4.67        12.16 
TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF 
       44.75         3.68        41.52        25.22         3.16        26.33 
TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX 
       21.01        47.93         3.16         4.90         7.13         7.43 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.75        12.92        16.47        13.55        13.22 
TCGA-L5-A8NN TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
        5.49        13.41        52.57        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.66        12.43        13.38        15.35        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR 
       12.59        12.49        12.76        12.85        15.52        13.22 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        12.00        12.23        12.03        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN 
       13.38        13.18         0.13        12.85        12.26         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC 
        5.06         7.04         6.35         9.30         2.89         2.30 
TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW 
       12.69         7.00        20.38         3.42        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I 
        8.12        52.27        46.19        18.05        11.24        15.91 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN 
       14.37         3.42         1.32        58.03        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 
        6.61         7.43        18.35         4.08         9.67        17.29 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 
        9.17        31.20         9.21        36.16        33.63        39.78 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       18.15        28.73         3.45         9.07        33.21        37.25 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        9.60        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 
        7.40        22.19        17.52        14.04        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
        5.39         9.21        20.22        26.73        24.79         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       20.88        10.68         7.53        34.98         1.48         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5802 TCGA-CD-5803 
        0.66        13.51         0.46        21.44        13.35        11.21 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.59        12.53        12.30        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.82        12.30        11.31        11.61        12.20        20.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 
        7.99         8.05        54.08         4.01        19.07        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       18.97         7.07        15.02        19.13        20.55        18.84 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8573 
       17.19        10.26        15.22        11.31        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A 
       18.21        21.14        16.44        11.31        22.29        19.96 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF 
        7.99        72.23        11.38        14.07        17.06         5.52 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       63.06        26.47         1.51         5.92        18.15        28.96 
TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       22.82        22.75        25.81         8.98         6.58         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        23.84        21.17        33.40        36.36 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       18.81        12.46         6.44         2.53         5.56        63.62 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 
        3.72        14.04        45.67        18.21         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 
       11.05        16.67        37.91       115.69         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         5.46        13.25        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       37.41        37.22         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X 
        2.70         1.87        73.41        39.45        42.64         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73        55.56         9.04         4.54        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       11.24        38.93        32.94        54.12 

$`DEL PEAK 13(4P16.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        5.16        20.02        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GR 
        0.23        20.15        25.78        31.27         7.63        32.45 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
        2.63         9.30         0.53        17.03        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A939 
       14.86        14.50       122.10        68.02        47.38        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-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       32.61        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE 
       29.00        15.48         2.60        25.12         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU 
        2.66        13.48         7.76        21.37         8.71        83.24 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V 
       10.85        10.36        13.41        12.33        13.15        12.59 
TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       13.25        12.59        22.39        11.54        12.33         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       25.25        10.52        12.03        33.11         7.82         7.59 
TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-AASV 
       16.31        38.40        53.95        15.78         5.29        15.35 
TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA7D TCGA-X8-AAAR 
       25.81        28.11        33.70        18.18         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       25.08        41.23         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-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7704 TCGA-BR-7707 
       40.21        30.90        44.94        21.90        35.24        35.84 
TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       15.32        29.56        14.43        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       32.25         8.05         0.56         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
        0.26         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
       31.27         7.36        25.05        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       27.12         9.34        28.14         6.28         7.53        31.96 
TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
       32.58         8.22        34.13        13.87         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.02        13.15        13.18        12.10        12.76 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 
        7.17        12.33        12.39        12.59        12.43         6.31 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 
       15.95         1.02        14.01        29.98         0.00         9.01 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       20.91        18.54        18.61        17.85        13.35        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       12.79        12.36        12.33        16.80        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        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13         0.62        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        22.29        59.54         5.03        13.58         0.56 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 
        6.21        77.29        52.21        30.51        24.39        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20         3.25        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.51        20.25        29.00        23.80        14.07        15.68 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45         3.39        18.38        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       37.64        36.95        19.73         8.52        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ 
       57.44        16.87        19.04         0.92        48.79        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PK 
       38.14        30.97        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        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       14.33        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       32.88         1.71        60.85         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        66.81         2.66        18.41        43.66        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        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE 
                         0.13                          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 
                       12.885                        15.480 
[1] "0.1 - 115.7 (12.9)" "0.0 - 122.3 (15.5)"
[1] "hr=" "1.2"
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4P16.3) MUTATED         4        7       16       14        45
  DEL PEAK 13(4P16.3) WILD-TYPE       6       14       31       19        42
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4P16.3) MUTATED          36        17         45         28
  DEL PEAK 13(4P16.3) WILD-TYPE        51        11         50         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 13(4P16.3) MUTATED           16       17         1
  DEL PEAK 13(4P16.3) WILD-TYPE         30       32         3
D51V3, multiclass
            clus
vv           DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  STAGE I                              4                             6
  STAGE IA                             7                            14
  STAGE IB                            16                            31
  STAGE II                            14                            19
  STAGE IIA                           45                            42
  STAGE IIB                           36                            51
  STAGE III                           17                            11
  STAGE IIIA                          45                            50
  STAGE IIIB                          28                            44
  STAGE IIIC                          16                            30
  STAGE IV                            17                            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 13(4P16.3) MUTATED      23  55 133  43
  DEL PEAK 13(4P16.3) WILD-TYPE    32  81 150  81
D51V4, multiclass
       clus
vv      DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  T0+T1                          23                            32
  T2                             55                            81
  T3                            133                           150
  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    88  86  45  32
  DEL PEAK 13(4P16.3) WILD-TYPE 119 101  53  64
D51V5, multiclass
    clus
vv   DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  N0                          88                           119
  N1                          86                           101
  N2                          45                            53
  N3                          32                            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"
D51V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED   232  12
  DEL PEAK 13(4P16.3) WILD-TYPE 292  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED    232   12
  DEL PEAK 13(4P16.3) WILD-TYPE  292   27
   clus
vv  DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  0                         232                           292
  1                          12                            27
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED    66 205
  DEL PEAK 13(4P16.3) WILD-TYPE 119 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED     66  205
  DEL PEAK 13(4P16.3) WILD-TYPE  119  235
        clus
vv       DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  FEMALE                          66                           119
  MALE                           205                           235
[1] 2 2
[1] FALSE
D51V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED   193  56
  DEL PEAK 13(4P16.3) WILD-TYPE 252  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED    193   56
  DEL PEAK 13(4P16.3) WILD-TYPE  252   63
     clus
vv    DEL PEAK 13(4P16.3) MUTATED DEL PEAK 13(4P16.3) WILD-TYPE
  NO                          193                           252
  YES                          56                            63
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(4P16.3) MUTATED      66                         6
  DEL PEAK 13(4P16.3) WILD-TYPE    68                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(4P16.3) MUTATED                                           0   169
  DEL PEAK 13(4P16.3) WILD-TYPE                                         1   223
D51V11, multiclass
                                           clus
vv                                          DEL PEAK 13(4P16.3) MUTATED
  ASIAN                                                              66
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             169
                                           clus
vv                                          DEL PEAK 13(4P16.3) WILD-TYPE
  ASIAN                                                                68
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                               cls
clus                              0   1
  DEL PEAK 13(4P16.3) MUTATED     5 174
  DEL PEAK 13(4P16.3) WILD-TYPE   6 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4P16.3) MUTATED      5  174
  DEL PEAK 13(4P16.3) WILD-TYPE    6  230
                        clus
vv                       DEL PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         174
                        clus
vv                       DEL PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           230
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 14(4P15.2) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4P15.2) MUTATED   149 111
  DEL PEAK 14(4P15.2) WILD-TYPE 205 134
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          260                           339 
  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                          111                           134 
$`DEL PEAK 14(4P15.2) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         8.94        24.00         4.70        35.97        27.12 
TCGA-CG-4444 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       47.05         0.23         9.86        26.93        25.78        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       58.55         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
       32.45        33.27        35.21         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       18.64         3.88         0.53         0.79        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C 
        4.67        12.16        44.75        47.38        25.22         3.16 
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-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        7.43         7.40         3.75        12.92        16.47        13.55 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         5.49         8.71        13.41        52.57        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R 
       10.36         5.92        10.45        12.66        12.43        13.38 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW 
       12.85        15.52        13.22        12.33        25.25        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 
       12.85        12.26         8.02         7.59         5.06         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP 
       20.38         3.42        16.44         9.27         8.98        27.09 
TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ 
       22.82        12.43         1.55        18.31         8.12        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T8 
       52.27        46.19        18.05        11.24        15.91        14.37 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        3.42         1.32        58.03        11.01         9.44         6.61 
TCGA-BR-4188 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6565 
        7.43         4.08         9.67         9.57        17.29         9.17 
TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 
       31.20         9.21        39.78        18.15        28.73         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 
       33.21        37.25         0.69         9.60         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        2.20        15.58         7.40        22.19        17.52        14.04 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 
       14.79         3.72         5.39         9.21        26.73        24.79 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88        10.68         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5799 
        0.72         0.66        13.51         0.46        21.44        13.02 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8532 
       13.35        11.21        12.59        12.53        12.30        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       15.39        12.07        12.82        12.30        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 
       19.07        12.03        18.97         7.07        30.97        15.02 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       19.13        20.55        17.19        10.26        15.22        11.31 
TCGA-D7-8573 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 
       19.50        21.14        16.44        11.31        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-HF-7133 
        7.99        11.38        14.07        17.06         5.52        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        18.15        28.96        22.82 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       22.75        25.81         8.98         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
       12.95        23.84        21.17        33.40        36.36        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.46         6.44         6.74         2.53         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 
       36.95        14.04        45.67        18.21         6.08         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 
       11.05        16.67        37.91       115.69         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E3 
        5.79         5.46        13.25        13.02        18.48        21.73 
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-A8PZ TCGA-VQ-A91A TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
        1.87        73.41        39.45        42.64         9.50         9.73 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6A 
        9.04         4.54        21.04        42.54        11.24        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6F 
       32.94        54.12 

$`DEL PEAK 14(4P15.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         4.31        19.99        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 
        0.36         5.16        20.02        21.99        22.98        79.07 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GK TCGA-IC-A6RE 
       16.24        20.15        27.35        31.27         7.63         7.69 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A7DP TCGA-IG-A97H 
        2.63         9.30        17.03        23.41        14.86        14.50 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
      122.10        68.02         3.68        41.52        21.70        23.18 
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        26.33 
TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       32.61        18.35         7.17         1.38        58.59        29.00 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       15.48         2.60        25.12         3.02        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49O 
       13.48         7.76        21.37        83.24        10.85        13.41 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.33        13.15        12.59        13.25        12.59        22.39 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A9FP 
       11.54        12.33         4.47        10.52        12.03        12.03 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
       33.11         7.82        16.31        38.40        53.95        15.78 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA7D 
        5.29        15.35        25.81        28.11        33.70         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       18.21        25.08        41.23         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-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4280 
       18.35        30.90         4.08         9.34         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       34.68        15.95        13.87        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        40.21        30.90        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       35.24        35.84        33.63        15.32         3.45        29.56 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
       29.42         6.18        31.10        13.08         0.26         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        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.05        25.18        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        31.96        32.58 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        8.22        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         8.98        14.17         0.53        28.34        32.52 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 
       13.15        13.18        12.10        12.76         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
       12.39        12.59        12.43         6.31        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 
       14.01        29.98         0.00         9.01        12.00         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 
        7.99        25.71        12.66        20.91        18.84        18.54 
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        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       26.43        11.24        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        8.38         4.34         7.13        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-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8244 
        0.56         6.21        77.29        52.21        30.51        24.39 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.10         6.51        20.25        29.00        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       15.68         3.45         3.39        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       37.64         3.72        19.73         8.52        74.53         4.60 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E2 
       57.44        16.87        19.04         0.92        48.79        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        14.33        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A923 
       20.81        32.88         1.71        60.85        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 
       55.43         6.58         5.72        66.81         2.66        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        28.41        17.13        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE 
                         0.13                          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 
                       12.725                        15.950 
[1] "0.1 - 115.7 (12.7)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.3"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4P15.2) MUTATED         4        4       16       16        46
  DEL PEAK 14(4P15.2) WILD-TYPE       6       17       31       17        41
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(4P15.2) MUTATED          34        16         41         29
  DEL PEAK 14(4P15.2) WILD-TYPE        53        12         54         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 14(4P15.2) MUTATED           20       18         1
  DEL PEAK 14(4P15.2) WILD-TYPE         26       31         3
D52V3, multiclass
            clus
vv           DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  STAGE I                              4                             6
  STAGE IA                             4                            17
  STAGE IB                            16                            31
  STAGE II                            16                            17
  STAGE IIA                           46                            41
  STAGE IIB                           34                            53
  STAGE III                           16                            12
  STAGE IIIA                          41                            54
  STAGE IIIB                          29                            43
  STAGE IIIC                          20                            26
  STAGE IV                            18                            31
  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      18  58 131  45
  DEL PEAK 14(4P15.2) WILD-TYPE    37  78 152  79
D52V4, multiclass
       clus
vv      DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  T0+T1                          18                            37
  T2                             58                            78
  T3                            131                           152
  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    84  83  43  38
  DEL PEAK 14(4P15.2) WILD-TYPE 123 104  55  58
D52V5, multiclass
    clus
vv   DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  N0                          84                           123
  N1                          83                           104
  N2                          43                            55
  N3                          38                            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"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED   228  13
  DEL PEAK 14(4P15.2) WILD-TYPE 296  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED    228   13
  DEL PEAK 14(4P15.2) WILD-TYPE  296   26
   clus
vv  DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  0                         228                           296
  1                          13                            26
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED    67 202
  DEL PEAK 14(4P15.2) WILD-TYPE 118 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED     67  202
  DEL PEAK 14(4P15.2) WILD-TYPE  118  238
        clus
vv       DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  FEMALE                          67                           118
  MALE                           202                           238
[1] 2 2
[1] FALSE
D52V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED   186  56
  DEL PEAK 14(4P15.2) WILD-TYPE 259  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED    186   56
  DEL PEAK 14(4P15.2) WILD-TYPE  259   63
     clus
vv    DEL PEAK 14(4P15.2) MUTATED DEL PEAK 14(4P15.2) WILD-TYPE
  NO                          186                           259
  YES                          56                            63
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(4P15.2) MUTATED      67                         6
  DEL PEAK 14(4P15.2) WILD-TYPE    67                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(4P15.2) MUTATED                                           0   162
  DEL PEAK 14(4P15.2) WILD-TYPE                                         1   230
D52V11, multiclass
                                           clus
vv                                          DEL PEAK 14(4P15.2) MUTATED
  ASIAN                                                              67
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             162
                                           clus
vv                                          DEL PEAK 14(4P15.2) WILD-TYPE
  ASIAN                                                                67
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                               cls
clus                              0   1
  DEL PEAK 14(4P15.2) MUTATED     5 171
  DEL PEAK 14(4P15.2) WILD-TYPE   6 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4P15.2) MUTATED      5  171
  DEL PEAK 14(4P15.2) WILD-TYPE    6  233
                        clus
vv                       DEL PEAK 14(4P15.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         171
                        clus
vv                       DEL PEAK 14(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           233
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 15(4Q22.1) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(4Q22.1) MUTATED   164 124
  DEL PEAK 15(4Q22.1) WILD-TYPE 190 121
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          288                           311 
  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                          124                           121 
$`DEL PEAK 15(4Q22.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       35.97        27.12        20.02        47.05        22.98        79.07 
TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23         9.86        26.93        25.78        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
        7.63         5.92        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L 
       32.45        33.27        35.21         0.85         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FH 
        0.79        12.82         4.67        12.16        44.75        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR 
       23.18        25.22         3.16         3.32         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59         4.90         7.13         7.43        15.48         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.75        55.50         2.66        12.92        13.48 
TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV 
       16.47        13.22         8.71        13.41        83.24        52.57 
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-A49U TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 
       13.38        15.35        13.25        12.46        12.59        12.76 
TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.85        12.33         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.00        13.18        12.33        13.18        12.85        12.26 
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        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
        9.30        15.78         2.30        12.69         7.00        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET 
       16.44         9.27         8.98        27.09        22.82         1.55 
TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 
       28.11        52.27        18.05        11.24        15.91        25.08 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN 
       14.37         3.42         2.66        58.03        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 
        6.61        18.35         4.08         9.67        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7957 
        9.17        40.21        31.20        39.78        18.15         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 
       33.21        37.25        14.43         0.69         9.60        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8364 
        2.66        19.96         2.20        15.58        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       17.52        14.04        14.79         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8690 
        9.21        20.22        27.12        24.79         9.86        10.68 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48         0.72         0.66        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.15        21.44         5.13        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       11.21        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A 
       11.64        15.39        12.07        12.82        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 
       11.61         6.58        12.20        20.02         3.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
        8.05        54.08         4.01        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
        7.07        30.97         0.99        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
       25.71        12.66        20.91        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 
       10.26        15.22        15.98        12.36        11.31        19.50 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       18.21        16.44        11.31        19.96         0.62         7.99 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       72.23        11.38         3.48        19.53        14.07        17.06 
TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 
       13.58         5.52         6.21        63.06         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GD 
       18.15        28.96        22.82         0.76         5.59        22.75 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       23.80        21.17        33.40        36.36        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A666 
       12.46         6.44         6.74        10.62         2.53        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       45.67        18.21         6.08         9.24        11.05         8.61 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT 
       16.67        37.91       115.69         8.94        35.61        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       13.25        13.02        18.48        43.36        21.73         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PY 
       46.26        12.79         2.70         9.27        13.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-A91Y 
       73.41        39.45        18.74        20.81         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 
       55.56         4.54         5.72        21.04        42.54        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        16.14        27.55        12.43 

$`DEL PEAK 15(4Q22.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-Q9-A6FU 
       15.68        34.85        19.99        22.82         0.36         5.16 
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GJ TCGA-IC-A6RE 
       21.99        16.24        20.15        27.35        58.55         7.69 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.78         2.63        20.12        18.64         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FD 
       23.41         9.96        14.86        14.50       122.10        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
       30.25         0.30        26.33        32.61        21.01        47.93 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OU TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NK 
       18.35         7.17        29.00        25.12         3.02        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49N TCGA-LN-A49P 
        7.76         5.49        21.37        10.85        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 
       13.15        12.59        12.62        12.49        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 
       15.52        11.54        13.22        12.23        12.03        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6Y0 
        0.13        12.03        33.11         7.82        16.31        53.95 
TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8ER 
        2.89         5.29         3.42        15.35        25.81        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7D 
       18.31         8.12        33.70        18.18        46.19         9.17 
TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-5816 
       18.21        41.23         2.10         1.32        19.73        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-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        13.68        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       30.90        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       35.84        33.63        15.32        28.73         3.45        29.56 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8297 
       11.44        29.59        32.25         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        31.27         7.36        25.05         1.12 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       12.79         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       31.96        32.58        20.88         8.22        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        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        28.34        32.52         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8529 
       16.14        13.41        13.18        12.10        12.76        12.30 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.59        12.43         6.31        12.30        11.77        12.62 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
       27.02        15.95         1.02        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-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        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       15.65         8.38         4.34         7.13        14.47        21.27 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-7132 TCGA-HF-7134 
       22.29        59.54         5.03         0.56        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 
       30.51        26.47        24.39        22.32        21.07        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       21.37        29.98         0.10         6.51        20.25        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       14.07        15.68         3.45        18.38        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51        11.70        15.75        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
       63.62        37.64        36.95         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       74.53         4.60         5.13       122.30        40.64       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-A8DU TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        5.46        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP 
       16.31        22.19         2.50        17.85         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        29.59        64.57        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 
       32.88         1.71        42.64        60.85         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        66.81         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        17.26         0.79 

  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE 
                         0.23                          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 
                       12.935                        15.750 
[1] "0.2 - 115.7 (12.9)" "0.0 - 122.3 (15.8)"
[1] "hr=" "1.3"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(4Q22.1) MUTATED         2        6       18       18        42
  DEL PEAK 15(4Q22.1) WILD-TYPE       8       15       29       15        45
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(4Q22.1) MUTATED          43        20         47         30
  DEL PEAK 15(4Q22.1) WILD-TYPE        44         8         48         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 15(4Q22.1) MUTATED           21       23         4
  DEL PEAK 15(4Q22.1) WILD-TYPE         25       26         0
D53V3, multiclass
            clus
vv           DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             6                            15
  STAGE IB                            18                            29
  STAGE II                            18                            15
  STAGE IIA                           42                            45
  STAGE IIB                           43                            44
  STAGE III                           20                             8
  STAGE IIIA                          47                            48
  STAGE IIIB                          30                            42
  STAGE IIIC                          21                            25
  STAGE IV                            23                            26
  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      18  65 148  50
  DEL PEAK 15(4Q22.1) WILD-TYPE    37  71 135  74
D53V4, multiclass
       clus
vv      DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  T0+T1                          18                            37
  T2                             65                            71
  T3                            148                           135
  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    88  96  51  43
  DEL PEAK 15(4Q22.1) WILD-TYPE 119  91  47  53
D53V5, multiclass
    clus
vv   DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  N0                          88                           119
  N1                          96                            91
  N2                          51                            47
  N3                          43                            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"
D53V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED   247  18
  DEL PEAK 15(4Q22.1) WILD-TYPE 277  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED    247   18
  DEL PEAK 15(4Q22.1) WILD-TYPE  277   21
   clus
vv  DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  0                         247                           277
  1                          18                            21
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED    78 220
  DEL PEAK 15(4Q22.1) WILD-TYPE 107 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED     78  220
  DEL PEAK 15(4Q22.1) WILD-TYPE  107  220
        clus
vv       DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  FEMALE                          78                           107
  MALE                           220                           220
[1] 2 2
[1] FALSE
D53V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED   206  62
  DEL PEAK 15(4Q22.1) WILD-TYPE 239  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED    206   62
  DEL PEAK 15(4Q22.1) WILD-TYPE  239   57
     clus
vv    DEL PEAK 15(4Q22.1) MUTATED DEL PEAK 15(4Q22.1) WILD-TYPE
  NO                          206                           239
  YES                          62                            57
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(4Q22.1) MUTATED      70                         9
  DEL PEAK 15(4Q22.1) WILD-TYPE    64                         8
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(4Q22.1) MUTATED                                           1   178
  DEL PEAK 15(4Q22.1) WILD-TYPE                                         0   214
D53V11, multiclass
                                           clus
vv                                          DEL PEAK 15(4Q22.1) MUTATED
  ASIAN                                                              70
  BLACK OR AFRICAN AMERICAN                                           9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             178
                                           clus
vv                                          DEL PEAK 15(4Q22.1) WILD-TYPE
  ASIAN                                                                64
  BLACK OR AFRICAN AMERICAN                                             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q22.1) MUTATED     6 184
  DEL PEAK 15(4Q22.1) WILD-TYPE   5 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q22.1) MUTATED      6  184
  DEL PEAK 15(4Q22.1) WILD-TYPE    5  220
                        clus
vv                       DEL PEAK 15(4Q22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         184
                        clus
vv                       DEL PEAK 15(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 16(4Q34.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(4Q34.3) MUTATED   166 124
  DEL PEAK 16(4Q34.3) WILD-TYPE 188 121
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          290                           309 
  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                          124                           121 
$`DEL PEAK 16(4Q34.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       60.39        18.28         4.31         8.94        24.00         4.70 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
        0.36        35.97        27.12         5.16        20.02        47.05 
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU 
       22.98        79.07        16.24         0.23         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO 
       26.93        25.78        14.30         5.92         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A50L 
        4.21        32.45        33.27         0.85         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93C 
        0.79        12.82        44.75        41.52        47.38        23.18 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS 
       25.22         3.16        18.35         3.32         3.16        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A891 
        4.90         7.13         7.43        15.48         7.40         3.75 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A6VZ 
        5.49         8.71        13.41        83.24        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49W 
        5.92        10.45        12.66        13.41        13.38        13.25 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        12.76        22.39        12.85        12.33         4.47 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        10.52        12.00        12.23        13.18        12.33 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.38        12.85        12.26         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.06         7.04        38.40         6.35         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00        20.38        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        8.98        27.09        22.82         1.55         8.12        28.11 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-ZR-A9CJ 
       18.18        52.27        18.05        15.91        25.08        19.73 
TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4257 
       58.03        19.56        11.01         9.44        18.35         9.67 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6803 
       17.29        19.33         9.17        25.61        12.16        31.20 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 
        9.21        35.24        33.63        18.15        28.73         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 
       33.21        37.25        14.43         0.69         9.60         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 
       19.96         2.20        15.58         7.40        31.10        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       17.52        14.04        14.79         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 
        9.21        20.22        26.73        24.79         9.86         7.53 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD 
       34.98         1.48         0.72         0.66        13.51        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        1.15        21.44        13.02        13.15        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.33        12.39 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A 
       11.64        15.39        12.07        12.82        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       11.61        12.20        20.02        27.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       54.08         4.01        19.07        12.03         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6518 
       30.97         6.97         1.02        15.02        12.66        19.13 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A4YU 
       11.31        12.33        19.50        18.21        14.27        16.44 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-5647 
       11.24        11.31        11.44        22.29        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
        7.99        11.38        19.53        14.07        17.06        13.58 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 
        5.52        63.06         1.51         5.92        18.15        22.82 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
        0.76        22.75         8.98         6.58         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        23.80        21.17        33.40        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       13.35        19.53         6.44         6.74        10.62        11.70 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53        63.62        36.95        14.04        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        43.36        21.73         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       22.19        12.79        13.35        64.57        73.41        39.45 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       18.74        32.88         1.71         9.50         9.73        55.56 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54        21.04        42.54        18.41        43.66        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       32.94        17.13        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 16(4Q34.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-CG-4460 TCGA-KB-A93G 
       15.68        34.85        19.99        22.82        21.99        20.15 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IC-A6RE TCGA-IG-A3QL 
       31.27        58.55         7.63        13.94         7.69        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D 
       20.78         2.63        20.12        18.64         9.30        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41         9.96        14.86         4.67        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F 
      122.10        68.02         3.68        21.70        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88W 
       47.93         7.17         1.38        29.00         2.60        25.12 
TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L7-A56G 
        3.02        13.55         7.76        21.37        52.57        10.85 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.43        12.33        13.15        15.35        12.59        12.62 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.46        12.49        12.59        15.52        11.54        13.22 
TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 
       25.25        12.03        13.18         0.13        12.03        33.11 
TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       16.31        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 
       25.81        12.43        18.31        33.70        46.19        11.24 
TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        18.21        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4183 
        1.32         2.66        26.70        11.70         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.97         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 
       13.87        13.68        39.12        26.10        32.78        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 
       36.16        35.84        39.78        15.32         3.45        29.56 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        6.18        13.08         0.26         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 
        3.32        11.80        31.27         7.36        25.05         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       13.87         6.08        27.55        28.57        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        28.34        32.52         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8529 
       16.14         5.13        13.41        13.18        12.10        12.30 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI 
       12.59        12.43         6.31        12.30         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 
       12.62         3.02        15.95         1.02        14.01        29.98 
TCGA-CG-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        25.71        20.91        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        12.36        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 
       36.43        13.78        14.76        26.43        20.32        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-FP-A9TM 
        3.48        22.29        59.54         5.03         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       77.29        52.21        30.51        26.47        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32        21.07        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-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-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.10         6.51        20.25        29.00        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RS 
       36.36         3.45        18.81         3.39        18.38        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        6.51        15.75        13.51         5.56        37.64         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 
       19.73        74.53         4.60         8.61         5.13        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA 
      115.69       116.38        71.38        57.44        16.87        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.79         5.46        37.41        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       34.29        16.31         2.50         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D 
        9.27        23.41        15.65        29.59        14.33        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 
       21.83        61.22        20.81        42.64        60.85         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        66.81         2.66 
TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-ZA-A8F6 
       11.24        28.41        17.26 

  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE 
                         0.23                          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 
                       13.235                        15.350 
[1] "0.2 - 122.3 (13.2)" "0.0 - 122.1 (15.3)"
[1] "hr=" "1.2"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(4Q34.3) MUTATED         2        6       20       22        39
  DEL PEAK 16(4Q34.3) WILD-TYPE       8       15       27       11        48
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(4Q34.3) MUTATED          37        20         46         39
  DEL PEAK 16(4Q34.3) WILD-TYPE        50         8         49         33
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 16(4Q34.3) MUTATED           26       16         3
  DEL PEAK 16(4Q34.3) WILD-TYPE         20       33         1
D54V3, multiclass
            clus
vv           DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             6                            15
  STAGE IB                            20                            27
  STAGE II                            22                            11
  STAGE IIA                           39                            48
  STAGE IIB                           37                            50
  STAGE III                           20                             8
  STAGE IIIA                          46                            49
  STAGE IIIB                          39                            33
  STAGE IIIC                          26                            20
  STAGE IV                            16                            33
  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  62 143  58
  DEL PEAK 16(4Q34.3) WILD-TYPE    36  74 140  66
D54V4, multiclass
       clus
vv      DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  T0+T1                          19                            36
  T2                             62                            74
  T3                            143                           140
  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    89  93  49  48
  DEL PEAK 16(4Q34.3) WILD-TYPE 118  94  49  48
D54V5, multiclass
    clus
vv   DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  N0                          89                           118
  N1                          93                            94
  N2                          49                            49
  N3                          48                            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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED   249  15
  DEL PEAK 16(4Q34.3) WILD-TYPE 275  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED    249   15
  DEL PEAK 16(4Q34.3) WILD-TYPE  275   24
   clus
vv  DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  0                         249                           275
  1                          15                            24
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED    85 215
  DEL PEAK 16(4Q34.3) WILD-TYPE 100 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED     85  215
  DEL PEAK 16(4Q34.3) WILD-TYPE  100  225
        clus
vv       DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  FEMALE                          85                           100
  MALE                           215                           225
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED   208  62
  DEL PEAK 16(4Q34.3) WILD-TYPE 237  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED    208   62
  DEL PEAK 16(4Q34.3) WILD-TYPE  237   57
     clus
vv    DEL PEAK 16(4Q34.3) MUTATED DEL PEAK 16(4Q34.3) WILD-TYPE
  NO                          208                           237
  YES                          62                            57
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(4Q34.3) MUTATED      68                         8
  DEL PEAK 16(4Q34.3) WILD-TYPE    66                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(4Q34.3) MUTATED                                           0   187
  DEL PEAK 16(4Q34.3) WILD-TYPE                                         1   205
D54V11, multiclass
                                           clus
vv                                          DEL PEAK 16(4Q34.3) MUTATED
  ASIAN                                                              68
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             187
                                           clus
vv                                          DEL PEAK 16(4Q34.3) WILD-TYPE
  ASIAN                                                                66
  BLACK OR AFRICAN AMERICAN                                             9
  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"
D54V12, binary
                               cls
clus                              0   1
  DEL PEAK 16(4Q34.3) MUTATED     5 183
  DEL PEAK 16(4Q34.3) WILD-TYPE   6 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(4Q34.3) MUTATED      5  183
  DEL PEAK 16(4Q34.3) WILD-TYPE    6  221
                        clus
vv                       DEL PEAK 16(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         183
                        clus
vv                       DEL PEAK 16(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 17(5Q12.1) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(5Q12.1) MUTATED   164 112
  DEL PEAK 17(5Q12.1) WILD-TYPE 190 133
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          276                           323 
  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                          112                           133 
$`DEL PEAK 17(5Q12.1) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG 
       60.39         4.31        24.00         4.70         0.36        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-MX-A663 
       27.12         5.16        20.02        47.05        22.98         9.86 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       27.35        25.78        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-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D 
       35.21         0.85         2.63         3.88         0.53        17.03 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
        4.67       122.10        44.75        47.38        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
       30.25        26.33        32.61        21.01        47.93         3.32 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88V 
        7.17         3.16        58.59         4.90         7.13         2.60 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        3.75         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       13.55         5.49        21.37         8.71        13.41        52.57 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N 
       46.09        10.85        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-A49Y 
       13.38        13.15        15.35        12.59        13.25        12.46 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.49        22.39        15.52        12.33         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-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       12.33        13.38        13.18        12.85        12.26        33.11 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 
        5.06        38.40         6.35        53.95         9.30         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
        2.30        12.69         3.42         9.27         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        22.82        12.43        18.31         8.12        28.11 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       52.27        11.24        15.91        25.08         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.66        19.73        58.03        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7704 
        6.61         9.67        19.33         9.17        12.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 
       33.63        39.78         3.45        29.56        33.21        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 
        0.69        29.42         2.66         2.20        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
        5.39         9.21        20.22        24.79         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       10.68        13.87         7.53        34.98         1.48         0.72 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       20.42         1.15        21.44        13.15        13.18        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82         6.31        12.30        11.31        11.61 
TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
       12.20        27.02         7.99         4.01        14.01        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5732 
       12.03        18.97        30.97        36.00        15.02        69.04 
TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       20.91        18.84        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-A6EV 
       15.98        12.79        11.31        12.33        24.72        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 
       11.31        22.29        15.65        19.96         0.62         7.99 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       72.23        19.53        17.06        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        6.21        63.06         1.51         5.92        18.15        28.96 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        0.76         5.59         3.25        22.75        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD 
        6.58         2.10        12.95        23.84        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36        18.81         3.39        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 
        6.44         6.74         6.51        10.62        15.75         2.53 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        37.64        36.95        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        8.52        37.91       115.69         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
       13.25        13.02        43.36        37.41         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS 
       22.19        12.79         2.70        17.85         1.87        13.35 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z 
       14.33        39.45        18.74         1.71         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 
        9.04         4.54         5.72        21.04        42.54        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       43.66        38.93        17.13        54.12        27.55         0.79 

$`DEL PEAK 17(5Q12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        34.85        18.28         8.94        19.99        22.82 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U 
       21.99        79.07        16.24         0.23        20.15        26.93 
TCGA-2H-A9GH TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
       31.27         7.69        20.78        20.12        18.64         9.30 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H 
        0.79        23.41        12.82         9.96        14.86        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       12.16        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4ON TCGA-L5-A4OQ 
       24.03         6.28         3.16         0.30        18.35         1.38 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NJ 
       29.00         7.43        15.48        25.12         7.40        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NU TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P 
       13.22         7.76        83.24        12.66        13.41        12.33 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A9 
       12.62        12.59        12.76        12.59        12.85        11.54 
TCGA-LN-A4MR TCGA-LN-A9FO TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.22         0.13        12.03         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       16.31         7.04        15.78         7.00        20.38         5.29 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       16.44        15.35         1.55        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       18.05         9.17        18.21        41.23        14.37         3.42 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
       28.73         9.07        37.25        14.43        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
       32.25         8.05         0.56        19.96        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
        7.36        25.05         3.72        25.18         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       31.96        32.58        20.88        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL 
        0.66        32.52        13.51         0.46        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8530 
        5.13        13.41        13.02        11.21        12.10        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG 
       12.59        11.64        15.39        12.43        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        8.05        54.08        29.98         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       12.00         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
      105.07        12.03        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        7.99        25.71        12.66        19.13        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61        17.85        12.36        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
       20.32         8.38         4.34         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       11.38         3.48        14.07        22.29        59.54         5.03 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 
       77.29        52.21        30.51        26.47        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        21.07        24.30        24.26        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
        0.26        29.00        23.80        14.07        15.68         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-MX-A5UG 
       12.46        12.59        11.70        13.51         5.56         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       19.73        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         5.13        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL 
       71.38        57.44        35.61        16.87        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       48.79        18.48        21.73        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        64.57        73.41        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       20.81        32.88        42.64        60.85         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 
       55.43         6.58        66.81         2.66        11.24        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        26.04        16.14        12.43        17.26 

  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE 
                         0.36                          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 
                       13.165                        15.650 
[1] "0.4 - 122.1 (13.2)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D55V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(5Q12.1) MUTATED         9        8       15       12        40
  DEL PEAK 17(5Q12.1) WILD-TYPE       1       13       32       21        47
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(5Q12.1) MUTATED          42        18         48         28
  DEL PEAK 17(5Q12.1) WILD-TYPE        45        10         47         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 17(5Q12.1) MUTATED           17       21         3
  DEL PEAK 17(5Q12.1) WILD-TYPE         29       28         1
D55V3, multiclass
            clus
vv           DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  STAGE I                              9                             1
  STAGE IA                             8                            13
  STAGE IB                            15                            32
  STAGE II                            12                            21
  STAGE IIA                           40                            47
  STAGE IIB                           42                            45
  STAGE III                           18                            10
  STAGE IIIA                          48                            47
  STAGE IIIB                          28                            44
  STAGE IIIC                          17                            29
  STAGE IV                            21                            28
  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      29  62 133  43
  DEL PEAK 17(5Q12.1) WILD-TYPE    26  74 150  81
D55V4, multiclass
       clus
vv      DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  T0+T1                          29                            26
  T2                             62                            74
  T3                            133                           150
  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    87  93  46  38
  DEL PEAK 17(5Q12.1) WILD-TYPE 120  94  52  58
D55V5, multiclass
    clus
vv   DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  N0                          87                           120
  N1                          93                            94
  N2                          46                            52
  N3                          38                            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"
D55V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED   233  18
  DEL PEAK 17(5Q12.1) WILD-TYPE 291  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED    233   18
  DEL PEAK 17(5Q12.1) WILD-TYPE  291   21
   clus
vv  DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  0                         233                           291
  1                          18                            21
[1] 2 2
[1] FALSE
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED    72 210
  DEL PEAK 17(5Q12.1) WILD-TYPE 113 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED     72  210
  DEL PEAK 17(5Q12.1) WILD-TYPE  113  230
        clus
vv       DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  FEMALE                          72                           113
  MALE                           210                           230
[1] 2 2
[1] FALSE
D55V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED   202  58
  DEL PEAK 17(5Q12.1) WILD-TYPE 243  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED    202   58
  DEL PEAK 17(5Q12.1) WILD-TYPE  243   61
     clus
vv    DEL PEAK 17(5Q12.1) MUTATED DEL PEAK 17(5Q12.1) WILD-TYPE
  NO                          202                           243
  YES                          58                            61
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(5Q12.1) MUTATED      68                         8
  DEL PEAK 17(5Q12.1) WILD-TYPE    66                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(5Q12.1) MUTATED                                           0   171
  DEL PEAK 17(5Q12.1) WILD-TYPE                                         1   221
D55V11, multiclass
                                           clus
vv                                          DEL PEAK 17(5Q12.1) MUTATED
  ASIAN                                                              68
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             171
                                           clus
vv                                          DEL PEAK 17(5Q12.1) WILD-TYPE
  ASIAN                                                                66
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q12.1) MUTATED     5 169
  DEL PEAK 17(5Q12.1) WILD-TYPE   6 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q12.1) MUTATED      5  169
  DEL PEAK 17(5Q12.1) WILD-TYPE    6  235
                        clus
vv                       DEL PEAK 17(5Q12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         169
                        clus
vv                       DEL PEAK 17(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 18(6P25.3) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(6P25.3) MUTATED   103  79
  DEL PEAK 18(6P25.3) WILD-TYPE 251 166
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          182                           417 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           79                           166 
$`DEL PEAK 18(6P25.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT 
       60.39         4.31         4.70         0.36        35.97        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-5727 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-2H-A9GI 
        5.16        20.02        79.07        16.24        27.35        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 
       58.55         7.63        13.94         8.94         4.21        33.27 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97I TCGA-JY-A6F8 
       18.64         3.88         0.53        23.41        12.16       122.10 
TCGA-JY-A93C TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4ON 
       23.18        31.56         3.16        30.25         0.30        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A8NF 
        3.32         7.17         1.38         3.16         7.13         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV 
       13.48        16.47        13.55        13.22        13.41        52.57 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49W 
       10.36         5.92        12.43        12.33        12.59        13.25 
TCGA-LN-A4A2 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.49        12.33        25.25        13.18        12.33        13.38 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 
       12.85        12.26        33.11         7.59        16.31         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.89        12.69        20.38         5.29         3.42 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ 
       15.35         9.27        12.43        18.31         8.12        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 
       18.05        11.24        25.08         2.66        19.73        26.70 
TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-6803 TCGA-BR-7716 
        6.97        17.29        19.33        12.16        31.20        39.78 
TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8485 TCGA-BR-8486 
        3.45         0.69         6.18        31.10         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       24.79         9.86         8.22        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5802 
        0.72        13.51        20.65         1.15        13.15        13.35 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
       12.59         7.17        11.64        12.82        12.30        11.31 
TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4466 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5728 
       12.43         8.05        18.97         1.02        12.03        65.10 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 
       13.35        15.22        15.98        11.31        11.44        15.65 
TCGA-D7-A74A TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A9TM 
       19.96        72.23        11.38        17.06        13.58         6.21 
TCGA-HF-7133 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4G3 
       63.06        30.51        26.47         5.92        22.82         5.59 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H6 
       22.75        11.77         8.98         6.58        12.95        21.17 
TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NU TCGA-KB-A6F5 
       33.40        12.46        13.35         6.74        11.70         5.56 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 
       36.95        45.67        18.21         6.08         9.24        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU 
      122.30       115.69        57.44         8.94         0.92         5.46 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.22         7.73        22.19         2.70        17.85         1.87 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 
       13.35        14.33        18.74        20.81        55.56         9.04 
TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G 
        5.72        42.54        43.66        38.93        54.12        26.04 
TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       16.14         0.79 

$`DEL PEAK 18(6P25.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI 
       15.68        34.85        18.28         8.94        24.00        19.99 
TCGA-L5-A88T TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       22.82        47.05        21.99        22.98         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GL TCGA-2H-A9GO 
        9.86        26.93        25.78        31.27         5.92        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       32.45         7.69        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        14.50        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        47.38        21.70        25.22        24.03         6.28 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OT 
       26.33        32.61        21.01        47.93        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       29.00         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN 
        3.75         3.02        55.50        12.92         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49L 
       21.37         8.71        83.24        46.09        10.85        10.45 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       12.66        13.41        13.38        13.15        15.35        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.76        12.59        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV 
       15.52        11.54        12.33        13.22         4.47        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.03        13.18         0.13        12.03 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02         5.06         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EO 
       53.95         2.30         7.00        16.44         8.98        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 
       27.09        22.82         1.55        28.11        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 
       46.19         9.17        15.91        18.21        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI 
        3.42         2.10         1.32        58.03        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-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
       18.35        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
       18.05        19.89         8.98        40.21        30.90        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.15        15.32        28.73         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        14.43        11.44        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         2.20 
TCGA-BR-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 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       25.18         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        6.28         7.53        26.73        31.96        32.58        20.88 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52         0.46        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.41        13.02        13.18        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 
       12.53        12.33        12.30        12.39        12.59        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.07        12.43         6.31        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
      105.07        15.02        28.96         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       25.71        20.91        18.61        17.85        17.19        10.26 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.24        20.32        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        7.13         0.62         7.99        14.47        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-A4BF TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        5.52        77.29        52.21         1.51        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       28.96        22.32        21.07         0.76        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       23.84        23.80        14.07        15.68        36.36         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        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 
        6.51        10.62        15.75        13.51         2.53        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60        11.05         8.61         5.13        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        35.61        16.87        19.04         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       48.79        13.25        13.02        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.41        38.14        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50        12.79         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
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        66.81        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        32.94        17.13 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          0.3                           0.0 
  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 
                         13.3                          14.5 
[1] "0.3 - 122.3 (13.3)" "0.0 - 116.4 (14.5)"
[1] "hr=" "1.1"
D56V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6P25.3) MUTATED         5        7        8        7        26
  DEL PEAK 18(6P25.3) WILD-TYPE       5       14       39       26        61
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6P25.3) MUTATED          27        12         28         20
  DEL PEAK 18(6P25.3) WILD-TYPE        60        16         67         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 18(6P25.3) MUTATED           14       13         2
  DEL PEAK 18(6P25.3) WILD-TYPE         32       36         2
D56V3, multiclass
            clus
vv           DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  STAGE I                              5                             5
  STAGE IA                             7                            14
  STAGE IB                             8                            39
  STAGE II                             7                            26
  STAGE IIA                           26                            61
  STAGE IIB                           27                            60
  STAGE III                           12                            16
  STAGE IIIA                          28                            67
  STAGE IIIB                          20                            52
  STAGE IIIC                          14                            32
  STAGE IV                            13                            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
  DEL PEAK 18(6P25.3) MUTATED      18  39  94  27
  DEL PEAK 18(6P25.3) WILD-TYPE    37  97 189  97
D56V4, multiclass
       clus
vv      DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  T0+T1                          18                            37
  T2                             39                            97
  T3                             94                           189
  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    60  55  30  29
  DEL PEAK 18(6P25.3) WILD-TYPE 147 132  68  67
D56V5, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  N0                          60                           147
  N1                          55                           132
  N2                          30                            68
  N3                          29                            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"
D56V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED   152   8
  DEL PEAK 18(6P25.3) WILD-TYPE 372  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED    152    8
  DEL PEAK 18(6P25.3) WILD-TYPE  372   31
   clus
vv  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  0                         152                           372
  1                           8                            31
[1] 2 2
[1] FALSE
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED    53 135
  DEL PEAK 18(6P25.3) WILD-TYPE 132 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     53  135
  DEL PEAK 18(6P25.3) WILD-TYPE  132  305
        clus
vv       DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  FEMALE                          53                           132
  MALE                           135                           305
[1] 2 2
[1] FALSE
D56V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED   128  41
  DEL PEAK 18(6P25.3) WILD-TYPE 317  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED    128   41
  DEL PEAK 18(6P25.3) WILD-TYPE  317   78
     clus
vv    DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  NO                          128                           317
  YES                          41                            78
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(6P25.3) MUTATED      40                         5
  DEL PEAK 18(6P25.3) WILD-TYPE    94                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(6P25.3) MUTATED                                           0   119
  DEL PEAK 18(6P25.3) WILD-TYPE                                         1   273
D56V11, multiclass
                                           clus
vv                                          DEL PEAK 18(6P25.3) MUTATED
  ASIAN                                                              40
  BLACK OR AFRICAN AMERICAN                                           5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             119
                                           clus
vv                                          DEL PEAK 18(6P25.3) WILD-TYPE
  ASIAN                                                                94
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               273
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED     5 111
  DEL PEAK 18(6P25.3) WILD-TYPE   6 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED      5  111
  DEL PEAK 18(6P25.3) WILD-TYPE    6  293
                        clus
vv                       DEL PEAK 18(6P25.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         111
                        clus
vv                       DEL PEAK 18(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           293
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 19(6Q16.3) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(6Q16.3) MUTATED    82  59
  DEL PEAK 19(6Q16.3) WILD-TYPE 272 186
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                          141                           458 
  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                           59                           186 
$`DEL PEAK 19(6Q16.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4475 TCGA-VQ-A8PU 
       60.39         8.94         0.36        20.02        22.98        27.35 
TCGA-2H-A9GF TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A50L TCGA-IG-A8O2 
       25.78         7.69        33.27        35.21         0.53         4.67 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4ON 
       14.50        44.75        47.38        25.22         3.16        18.35 
TCGA-L5-A4OR TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU 
        3.16        16.47        13.55        13.22        13.41        83.24 
TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 
       52.57         5.92        13.38        13.25        12.62        12.59 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A8HZ 
       22.39        12.33        13.22        12.33        25.25        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6XG 
       13.18         0.13        12.26         8.02         5.06        38.40 
TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EQ 
        2.89        12.69        20.38         3.42         9.27        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-XP-A8T8 
       12.43        18.31         8.12        28.11        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6456 
        3.42         2.10        19.73        18.35         6.18        17.29 
TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 
        9.17        39.78        15.32         3.45        29.56        14.43 
TCGA-BR-8080 TCGA-BR-8486 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        9.60        20.22         0.53        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        1.15        11.21        12.10        12.30        12.39        11.64 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.39        12.82         6.31         8.05        14.01        29.98 
TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       12.03        36.00         1.02        15.02        69.04        12.66 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-8570 
       18.84        18.54        13.35        17.19        15.98        24.72 
TCGA-D7-8576 TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C 
       14.66        13.78        11.31        15.65        19.96        11.38 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-A4GD 
       19.53        17.06        13.58         0.56        26.47        22.75 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS 
       23.84        23.80        36.36        13.35         6.44        12.59 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93J TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MV 
       10.62        11.70        36.95        18.21         6.08       122.30 
TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH 
       57.44        19.04        18.48         7.73        46.26        12.79 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A923 
       13.35        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        43.66        54.12        16.14 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        17.26         0.79 

$`DEL PEAK 19(6Q16.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 
       19.99        22.82        35.97        27.12         5.16        47.05 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        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-A3Y9 
       13.94         8.94        16.24         4.21        32.45         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-A939 
       12.16       122.10        68.02         3.68        41.52        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-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        21.01        47.93         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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
       15.48         2.60        25.12         7.40         3.75         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN 
       55.50         2.66        12.92        13.48         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       21.37         8.71        46.09        10.85        10.36        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       12.66        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.59        12.46        12.49        12.76        12.59        12.85 
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-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       12.03        13.18        13.38        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.82         7.59        16.31         7.04         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30        15.78         2.30         7.00         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EY 
       15.35         8.98        25.81        27.09         1.55        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       18.18        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       15.91        18.21        41.23         1.32         2.66        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        13.68        19.33        39.12        26.10 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 
       36.16        35.24        35.84        33.63        18.15        28.73 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        9.07        33.21        37.25        11.44         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       32.25         8.05         0.56        29.42         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.98         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        0.72        14.17        28.34         0.66        32.52         0.46 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18        13.35        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
       12.33        12.59        12.07        12.43        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-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-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       54.08         4.01        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
        7.07        12.00        30.97         6.97         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-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        20.91        19.13        20.55 
TCGA-D7-6522 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        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        16.80        19.50        17.19        18.21 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
        5.03         5.52         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       30.51         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        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         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        29.00        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V 
       18.38        12.46        19.53         6.74         6.51        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       13.51         2.53         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
       19.73        14.04        45.67         8.52        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        9.24        11.05         8.61         5.13        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.87         5.79         0.92        48.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.02        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       30.97        34.29        16.31        22.19         2.50         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.56        55.43         6.58         5.72        66.81         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6K 
       26.04        12.43 

  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE 
                         0.13                          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 
                        14.33                         13.87 
[1] "0.1 - 122.3 (14.3)" "0.0 - 122.1 (13.9)"
[1] "hr=" "1"  
D57V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q16.3) MUTATED         1        5       10        8        19
  DEL PEAK 19(6Q16.3) WILD-TYPE       9       16       37       25        68
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q16.3) MUTATED          25        10         22         16
  DEL PEAK 19(6Q16.3) WILD-TYPE        62        18         73         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 19(6Q16.3) MUTATED            7        7         1
  DEL PEAK 19(6Q16.3) WILD-TYPE         39       42         3
D57V3, multiclass
            clus
vv           DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             5                            16
  STAGE IB                            10                            37
  STAGE II                             8                            25
  STAGE IIA                           19                            68
  STAGE IIB                           25                            62
  STAGE III                           10                            18
  STAGE IIIA                          22                            73
  STAGE IIIB                          16                            56
  STAGE IIIC                           7                            39
  STAGE IV                             7                            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 19(6Q16.3) MUTATED      13  37  69  18
  DEL PEAK 19(6Q16.3) WILD-TYPE    42  99 214 106
D57V4, multiclass
       clus
vv      DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  T0+T1                          13                            42
  T2                             37                            99
  T3                             69                           214
  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    46  49  23  17
  DEL PEAK 19(6Q16.3) WILD-TYPE 161 138  75  79
D57V5, multiclass
    clus
vv   DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  N0                          46                           161
  N1                          49                           138
  N2                          23                            75
  N3                          17                            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"
D57V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED   121   4
  DEL PEAK 19(6Q16.3) WILD-TYPE 403  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED    121    4
  DEL PEAK 19(6Q16.3) WILD-TYPE  403   35
   clus
vv  DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  0                         121                           403
  1                           4                            35
[1] 2 2
[1] FALSE
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED    32 115
  DEL PEAK 19(6Q16.3) WILD-TYPE 153 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED     32  115
  DEL PEAK 19(6Q16.3) WILD-TYPE  153  325
        clus
vv       DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  FEMALE                          32                           153
  MALE                           115                           325
[1] 2 2
[1] FALSE
D57V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED    95  34
  DEL PEAK 19(6Q16.3) WILD-TYPE 350  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED     95   34
  DEL PEAK 19(6Q16.3) WILD-TYPE  350   85
     clus
vv    DEL PEAK 19(6Q16.3) MUTATED DEL PEAK 19(6Q16.3) WILD-TYPE
  NO                           95                           350
  YES                          34                            85
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(6Q16.3) MUTATED      33                         7
  DEL PEAK 19(6Q16.3) WILD-TYPE   101                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(6Q16.3) MUTATED                                           0    89
  DEL PEAK 19(6Q16.3) WILD-TYPE                                         1   303
D57V11, multiclass
                                           clus
vv                                          DEL PEAK 19(6Q16.3) MUTATED
  ASIAN                                                              33
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              89
                                           clus
vv                                          DEL PEAK 19(6Q16.3) WILD-TYPE
  ASIAN                                                               101
  BLACK OR AFRICAN AMERICAN                                            10
  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"
D57V12, binary
                               cls
clus                              0   1
  DEL PEAK 19(6Q16.3) MUTATED     3  92
  DEL PEAK 19(6Q16.3) WILD-TYPE   8 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6Q16.3) MUTATED      3   92
  DEL PEAK 19(6Q16.3) WILD-TYPE    8  312
                        clus
vv                       DEL PEAK 19(6Q16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 19(6Q16.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 20(6Q26) MUTATION ANALYSIS
D58V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(6Q26) MUTATED    86  62
  DEL PEAK 20(6Q26) WILD-TYPE 268 183
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                        148                         451 
  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                         62                         183 
$`DEL PEAK 20(6Q26) MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y TCGA-FP-A8CX TCGA-MX-A663 
       34.85         4.31         8.94         0.36         0.23         9.86 
TCGA-2H-A9GF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FH 
       25.78        33.27        35.21         4.67        14.50        47.38 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OR TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.22         3.16         3.16         7.40        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49K 
       13.55        13.22        13.41        83.24        52.57         5.92 
TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.38        13.25        12.62        12.59        12.49        12.76 
TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       22.39        12.33        13.22        25.25        12.00        12.23 
TCGA-LN-A8HZ TCGA-R6-A6DN TCGA-R6-A6XG TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
       12.33         8.02        38.40         2.30        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EW 
        3.42        16.44         9.27        22.82        12.43         8.12 
TCGA-VR-A8EX TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-BR-4183 
       28.11        25.08         3.42        19.73        19.56         6.61 
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       19.33         9.17        12.16        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8680 TCGA-BR-A4IY 
       28.73        29.56         0.69         9.60        31.96        12.89 
TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-5804 
       13.51        20.42         1.15        13.15        11.21        12.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
       12.30        12.39        11.64        15.39        12.82         6.31 
TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 
       12.30         3.02        15.95         8.05         4.01        29.98 
TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 
       12.03         7.07        12.00         6.97         1.02        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       15.02        69.04        12.66        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX 
       17.19        24.72        19.50        18.21        14.66        11.31 
TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
       11.44        15.65        19.96        11.38        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-A4G3 TCGA-HU-A4GU 
        0.56         5.52        63.06        26.47         5.59         6.58 
TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       23.84        33.40        13.35         6.44        10.62        11.70 
TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MV 
       36.95        45.67        18.21         6.08        16.67       122.30 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 
       57.44         8.94         0.92        13.02        43.36         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PF TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A91Z 
       46.26         2.50        13.35        14.33        20.81        55.56 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6D 
        2.01         4.54        21.04        42.54        43.66        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       54.12        16.14        27.55         0.79 

$`DEL PEAK 20(6Q26) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        18.28        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
       22.82        35.97        27.12         5.16        20.02        47.05 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-VQ-A8PU 
       21.99        22.98        79.07        16.24        20.15        27.35 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        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-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-A6FD 
        9.96        14.86        12.16       122.10        44.75        68.02 
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-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28        30.25         0.30        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       47.93        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A56G 
        7.76         5.49        21.37         8.71        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.15        15.35        12.59        12.46        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HY 
       15.52        11.54         4.47        12.33        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.26        33.11         7.82         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP 
        7.00         5.29        15.35         8.98        25.81        27.09 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55        18.31        33.70        18.18        52.27        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        18.21        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
       14.37         2.10         1.32         2.66        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 
       11.70        11.01         9.47         9.44         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        44.94        21.90         9.21        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       35.84        33.63         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        11.44        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        26.33         4.31        14.04         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        9.34        28.14         6.28         7.53        26.73        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       13.87         7.53         6.08        34.98         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        32.52         0.46        20.65        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 
        5.13        13.41        13.02        13.18        13.35        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8534 
       12.59        12.53         7.17        12.33        12.59        12.07 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.43        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 
       11.77        12.62        20.02        27.02         1.02         7.99 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       54.08        14.01        19.07         0.00         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       30.97        36.00         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       20.91        19.13        18.84        18.61        17.85        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        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       20.32        22.29         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.99        14.47        72.23        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 
       14.07        22.29        59.54         5.03         6.21        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       52.21        30.51         1.51         5.92        24.39        18.15 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       24.26        22.68        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       20.25         0.26         2.10        12.95        29.00        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39        18.38        12.46        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.51        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI 
       37.64         3.72        19.73        14.04         8.52        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW 
        4.60         9.24        11.05         8.61         5.13        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        35.61        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 
       19.04         5.79        48.79         5.46        13.25        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       16.31        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        18.74        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
        1.71        42.64        60.85         9.50         9.73         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        66.81         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        28.41        38.93        32.94        26.04        12.43 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE 
                       0.23                        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 
                      13.30                       14.37 
[1] "0.2 - 122.3 (13.3)" "0.0 - 122.1 (14.4)"
[1] "hr=" "1.1"
D58V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(6Q26) MUTATED         0        2        7       10        24
  DEL PEAK 20(6Q26) WILD-TYPE      10       19       40       23        63
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(6Q26) MUTATED          18        11         23         18
  DEL PEAK 20(6Q26) WILD-TYPE        69        17         72         54
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 20(6Q26) MUTATED            9       14         1
  DEL PEAK 20(6Q26) WILD-TYPE         37       35         3
D58V3, multiclass
            clus
vv           DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  STAGE I                            0                          10
  STAGE IA                           2                          19
  STAGE IB                           7                          40
  STAGE II                          10                          23
  STAGE IIA                         24                          63
  STAGE IIB                         18                          69
  STAGE III                         11                          17
  STAGE IIIA                        23                          72
  STAGE IIIB                        18                          54
  STAGE IIIC                         9                          37
  STAGE IV                          14                          35
  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  31  83  23
  DEL PEAK 20(6Q26) WILD-TYPE    48 105 200 101
D58V4, multiclass
       clus
vv      DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  T0+T1                         7                          48
  T2                           31                         105
  T3                           83                         200
  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    46  46  25  25
  DEL PEAK 20(6Q26) WILD-TYPE 161 141  73  71
D58V5, multiclass
    clus
vv   DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  N0                        46                         161
  N1                        46                         141
  N2                        25                          73
  N3                        25                          71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED   124   9
  DEL PEAK 20(6Q26) WILD-TYPE 400  30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED    124    9
  DEL PEAK 20(6Q26) WILD-TYPE  400   30
   clus
vv  DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  0                       124                         400
  1                         9                          30
[1] 2 2
[1] FALSE
D58V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED    36 116
  DEL PEAK 20(6Q26) WILD-TYPE 149 324
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED     36  116
  DEL PEAK 20(6Q26) WILD-TYPE  149  324
        clus
vv       DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  FEMALE                        36                         149
  MALE                         116                         324
[1] 2 2
[1] FALSE
D58V8, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED   101  31
  DEL PEAK 20(6Q26) WILD-TYPE 344  88
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED    101   31
  DEL PEAK 20(6Q26) WILD-TYPE  344   88
     clus
vv    DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  NO                        101                         344
  YES                        31                          88
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(6Q26) MUTATED      35                         6
  DEL PEAK 20(6Q26) WILD-TYPE    99                        11
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(6Q26) MUTATED                                           0    88
  DEL PEAK 20(6Q26) WILD-TYPE                                         1   304
D58V11, multiclass
                                           clus
vv                                          DEL PEAK 20(6Q26) MUTATED
  ASIAN                                                            35
  BLACK OR AFRICAN AMERICAN                                         6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            88
                                           clus
vv                                          DEL PEAK 20(6Q26) WILD-TYPE
  ASIAN                                                              99
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             304
[1] 4 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, binary
                             cls
clus                            0   1
  DEL PEAK 20(6Q26) MUTATED     3  91
  DEL PEAK 20(6Q26) WILD-TYPE   8 313
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(6Q26) MUTATED      3   91
  DEL PEAK 20(6Q26) WILD-TYPE    8  313
                        clus
vv                       DEL PEAK 20(6Q26) MUTATED DEL PEAK 20(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             3                           8
  NOT HISPANIC OR LATINO                        91                         313
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 21(7Q31.1) MUTATION ANALYSIS
D59V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q31.1) MUTATED    70  54
  DEL PEAK 21(7Q31.1) WILD-TYPE 284 191
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                          124                           475 
  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                           54                           191 
$`DEL PEAK 21(7Q31.1) MUTATED`
TCGA-L5-A43I TCGA-L5-A88Y TCGA-CG-4475 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       18.28         0.36        22.98        26.93        25.78        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        7.63         5.92         8.94         4.21        32.45         7.69 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
        0.85         2.63        20.12         3.88        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM 
        9.96         4.67        47.38         3.16        26.33        47.93 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE 
        3.16        29.00        15.48         2.60        25.12        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR 
        2.66        12.92        13.48        16.47        13.55         8.71 
TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       10.36        12.43        13.38        13.25        12.62        12.46 
TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MR TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ 
       12.76        12.85        13.22         0.13        33.11         5.06 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
       15.78         2.89         5.29         8.98        22.82         1.55 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-AAPN TCGA-BR-4255 TCGA-BR-6564 
       18.05         9.17        15.91         2.66         4.08        26.10 
TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8678 
       18.05        28.73         6.18        31.10        14.04        24.79 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8527 
        7.53         1.48         1.15        21.44        12.76         7.17 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CG-4301 TCGA-CG-4437 
       12.07         6.31        12.30        11.31         3.02         8.05 
TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4472 TCGA-D7-6815 TCGA-D7-6820 
       54.08        19.07        12.03        12.00        15.98        11.31 
TCGA-D7-8575 TCGA-D7-A4YX TCGA-D7-A6EX TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8631 
       18.21        36.43        11.31        72.23        19.53         0.56 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       22.75        11.77         6.58        12.95        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN 
       14.07        33.40        18.81         3.39        18.38        19.53 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-RD-A7BT TCGA-RD-A8MW 
       15.75         2.53        37.64        36.95         8.61        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 
        8.94        35.61         5.46        13.02        18.48        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-AA68 
        7.73        13.35        20.81         2.01         5.72        43.66 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       17.13        54.12        26.04        16.14 

$`DEL PEAK 21(7Q31.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       20.02        47.05        21.99        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM 
       20.15         9.86        27.35        31.27        58.55        13.94 
TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT 
       16.24        33.27        35.21        20.78        18.64         9.30 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
        0.53        23.41        12.82        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        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-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
        0.30        32.61        21.01        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Z 
        1.38        58.59         4.90         7.13         7.43         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        3.75         3.02        13.22         7.76         5.49        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
       13.41        83.24        52.57        46.09        10.85         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.66        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 
       12.59        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-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18        12.03        12.85        12.26         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC 
        9.30         2.30        12.69         7.00        20.38         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       16.44        15.35         9.27        25.81        27.09        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       46.19        11.24        18.21        25.08        41.23        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
        3.42         2.10         1.32        19.73        58.03        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-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-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 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        8.05         0.56        29.42         2.66        19.96         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-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51         0.46        20.65        20.42        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A48A 
       12.59        11.64        15.39        12.82        12.43        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        11.77        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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 
       29.98         0.00         9.01        18.97         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        10.26        15.22        12.79        12.36 
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-A4YY 
       21.14        20.91        14.27        16.44         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.99        14.47        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ 
       29.00        23.80        15.68        36.36         3.45        12.46 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
       11.70        13.51         5.56        63.62         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        57.44        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       19.04         5.79         0.92        48.79        13.25        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        37.41        38.14        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        55.56         9.04        55.43         4.54         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        38.93        32.94        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE 
                         0.13                          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 
                        13.12                         14.33 
[1] "0.1 - 72.2 (13.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D59V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q31.1) MUTATED         1        5        4        9        19
  DEL PEAK 21(7Q31.1) WILD-TYPE       9       16       43       24        68
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q31.1) MUTATED          21        15         22          9
  DEL PEAK 21(7Q31.1) WILD-TYPE        66        13         73         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 21(7Q31.1) MUTATED            5        8         2
  DEL PEAK 21(7Q31.1) WILD-TYPE         41       41         2
D59V3, multiclass
            clus
vv           DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             5                            16
  STAGE IB                             4                            43
  STAGE II                             9                            24
  STAGE IIA                           19                            68
  STAGE IIB                           21                            66
  STAGE III                           15                            13
  STAGE IIIA                          22                            73
  STAGE IIIB                           9                            63
  STAGE IIIC                           5                            41
  STAGE IV                             8                            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
  DEL PEAK 21(7Q31.1) MUTATED      14  23  71  14
  DEL PEAK 21(7Q31.1) WILD-TYPE    41 113 212 110
D59V4, multiclass
       clus
vv      DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  T0+T1                          14                            41
  T2                             23                           113
  T3                             71                           212
  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  53  21  12
  DEL PEAK 21(7Q31.1) WILD-TYPE 171 134  77  84
D59V5, multiclass
    clus
vv   DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  N0                          36                           171
  N1                          53                           134
  N2                          21                            77
  N3                          12                            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"
D59V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED   106   5
  DEL PEAK 21(7Q31.1) WILD-TYPE 418  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED    106    5
  DEL PEAK 21(7Q31.1) WILD-TYPE  418   34
   clus
vv  DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  0                         106                           418
  1                           5                            34
[1] 2 2
[1] FALSE
D59V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED    23 104
  DEL PEAK 21(7Q31.1) WILD-TYPE 162 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED     23  104
  DEL PEAK 21(7Q31.1) WILD-TYPE  162  336
        clus
vv       DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  FEMALE                          23                           162
  MALE                           104                           336
[1] 2 2
[1] FALSE
D59V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED    93  23
  DEL PEAK 21(7Q31.1) WILD-TYPE 352  96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED     93   23
  DEL PEAK 21(7Q31.1) WILD-TYPE  352   96
     clus
vv    DEL PEAK 21(7Q31.1) MUTATED DEL PEAK 21(7Q31.1) WILD-TYPE
  NO                           93                           352
  YES                          23                            96
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(7Q31.1) MUTATED      27                         3
  DEL PEAK 21(7Q31.1) WILD-TYPE   107                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(7Q31.1) MUTATED                                           1    75
  DEL PEAK 21(7Q31.1) WILD-TYPE                                         0   317
D59V11, multiclass
                                           clus
vv                                          DEL PEAK 21(7Q31.1) MUTATED
  ASIAN                                                              27
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK 21(7Q31.1) WILD-TYPE
  ASIAN                                                               107
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  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"
D59V12, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q31.1) MUTATED     1  69
  DEL PEAK 21(7Q31.1) WILD-TYPE  10 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q31.1) MUTATED      1   69
  DEL PEAK 21(7Q31.1) WILD-TYPE   10  335
                        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                                10
  NOT HISPANIC OR LATINO                           335
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 22(7Q36.3) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(7Q36.3) MUTATED    95  66
  DEL PEAK 22(7Q36.3) WILD-TYPE 259 179
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                          161                           438 
  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                           66                           179 
$`DEL PEAK 22(7Q36.3) MUTATED`
TCGA-L5-A43I TCGA-L5-A88Y TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-2H-A9GF 
       18.28         0.36        22.98        16.24        26.93        25.78 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         7.63         5.92         8.94        16.24         4.21 
TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A51D TCGA-IG-A5B8 
        7.69         0.85        20.12        18.64        17.03         0.79 
TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH 
        9.96        14.50        44.75        68.02         3.68        47.38 
TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       25.22         3.16        26.33        47.93        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A8NE 
        3.16        58.59        29.00         7.13        15.48        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NR TCGA-L7-A6VZ 
        2.66        12.92        13.48        13.55         8.71        10.36 
TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A49Y 
       10.45        13.41        13.38        13.15        12.62        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        12.76        12.85        12.33        13.22        25.25 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8W5 TCGA-V5-A7RB 
       33.11         7.82         5.06        38.40        15.78         5.29 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7B 
        8.98        25.81        12.43         1.55        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TN 
        9.17        15.91         3.42         2.66        19.56         9.44 
TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7704 TCGA-BR-7723 
        4.08        17.29        19.33        26.10        35.24        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8296 TCGA-BR-8369 TCGA-BR-8485 
        3.45        11.44         0.69        15.58        14.04         9.21 
TCGA-BR-8678 TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
       24.79         1.48         1.15        13.35        12.76        12.59 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       12.33        12.30        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-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-5724 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 
       12.03        12.00        12.03        20.55        13.35        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV 
       15.98        12.79        12.36        11.31        18.21        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-FP-7829 TCGA-FP-8631 TCGA-HU-8243 
       11.31        22.29        19.96        19.53         0.56         5.92 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       22.75        11.77         6.58        12.95        23.84        21.17 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40         3.45        18.81         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-KB-A93H 
       19.53         6.44         6.74        10.62        15.75        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU 
       14.04        45.67        18.21        37.91        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       13.02        18.48        37.22         7.73         2.70        17.85 
TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-AA64 
       13.35        18.74        20.81         5.72        66.81        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       43.66        54.12        26.04        16.14         0.79 

$`DEL PEAK 22(7Q36.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        34.85         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.70        19.99        22.82        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        47.05        21.99        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GR 
        9.86        27.35        31.27        58.55        13.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT 
       33.27        35.21        20.78         2.63         3.88         9.30 
TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I 
        0.53        23.41        12.82        14.86         4.67        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F 
      122.10        41.52        21.70        23.18        31.56        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
        6.28        30.25         0.30        32.61        21.01         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        1.38         4.90         7.43         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.75         3.02        16.47        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
       21.37        13.41        83.24        52.57        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V 
        5.92        12.66        12.43        12.33        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 
       13.25        12.49        12.59        22.39        15.52        11.54 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
        4.47        12.33        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       13.18        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26         8.02         7.59        16.31         7.04 
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         2.30        12.69 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         3.42        16.44        15.35         9.27 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       27.09        22.82        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.18        52.27        46.19        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
       14.37         2.10         1.32        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 
       11.70        11.01         9.47         6.61         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
        7.43        18.35        30.90         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        15.32         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       37.25        14.43        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.56        29.42         2.66        19.96         2.20         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        6.28         7.53        26.73        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08        34.98        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.18        11.21 
TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.10        12.53         7.17        12.39        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       15.39        12.43        12.43         6.58        12.20        11.77 
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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        29.98         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.26        15.22        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-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       20.32        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       14.07        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        5.52         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RL 
       29.00        23.80        14.07        15.68        36.36        13.35 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       12.59         6.51        11.70        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI 
       63.62        36.95         3.72        19.73         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79        13.25        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       12.79         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       61.22        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
        9.73        55.56         9.04         2.01        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 
        6.58        21.04         2.66        42.54        11.24        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       38.93        32.94        17.13        27.55        12.43        17.26 

  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE 
                         0.36                          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 
                        13.15                         14.45 
[1] "0.4 - 68.0 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D60V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(7Q36.3) MUTATED         1        6        5        9        23
  DEL PEAK 22(7Q36.3) WILD-TYPE       9       15       42       24        64
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(7Q36.3) MUTATED          33        14         27         11
  DEL PEAK 22(7Q36.3) WILD-TYPE        54        14         68         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 22(7Q36.3) MUTATED           10       13         3
  DEL PEAK 22(7Q36.3) WILD-TYPE         36       36         1
D60V3, multiclass
            clus
vv           DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  STAGE I                              1                             9
  STAGE IA                             6                            15
  STAGE IB                             5                            42
  STAGE II                             9                            24
  STAGE IIA                           23                            64
  STAGE IIB                           33                            54
  STAGE III                           14                            14
  STAGE IIIA                          27                            68
  STAGE IIIB                          11                            61
  STAGE IIIC                          10                            36
  STAGE IV                            13                            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 22(7Q36.3) MUTATED      17  32  86  24
  DEL PEAK 22(7Q36.3) WILD-TYPE    38 104 197 100
D60V4, multiclass
       clus
vv      DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  T0+T1                          17                            38
  T2                             32                           104
  T3                             86                           197
  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  61  26  23
  DEL PEAK 22(7Q36.3) WILD-TYPE 161 126  72  73
D60V5, multiclass
    clus
vv   DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  N0                          46                           161
  N1                          61                           126
  N2                          26                            72
  N3                          23                            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"
D60V6, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED   135  12
  DEL PEAK 22(7Q36.3) WILD-TYPE 389  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED    135   12
  DEL PEAK 22(7Q36.3) WILD-TYPE  389   27
   clus
vv  DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  0                         135                           389
  1                          12                            27
[1] 2 2
[1] FALSE
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED    42 123
  DEL PEAK 22(7Q36.3) WILD-TYPE 143 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED     42  123
  DEL PEAK 22(7Q36.3) WILD-TYPE  143  317
        clus
vv       DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  FEMALE                          42                           143
  MALE                           123                           317
[1] 2 2
[1] FALSE
D60V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED   118  33
  DEL PEAK 22(7Q36.3) WILD-TYPE 327  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED    118   33
  DEL PEAK 22(7Q36.3) WILD-TYPE  327   86
     clus
vv    DEL PEAK 22(7Q36.3) MUTATED DEL PEAK 22(7Q36.3) WILD-TYPE
  NO                          118                           327
  YES                          33                            86
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(7Q36.3) MUTATED      36                         2
  DEL PEAK 22(7Q36.3) WILD-TYPE    98                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(7Q36.3) MUTATED                                           0   102
  DEL PEAK 22(7Q36.3) WILD-TYPE                                         1   290
D60V11, multiclass
                                           clus
vv                                          DEL PEAK 22(7Q36.3) MUTATED
  ASIAN                                                              36
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             102
                                           clus
vv                                          DEL PEAK 22(7Q36.3) WILD-TYPE
  ASIAN                                                                98
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               290
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 22(7Q36.3) MUTATED     2  97
  DEL PEAK 22(7Q36.3) WILD-TYPE   9 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(7Q36.3) MUTATED      2   97
  DEL PEAK 22(7Q36.3) WILD-TYPE    9  307
                        clus
vv                       DEL PEAK 22(7Q36.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK 22(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           307
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 23(8P23.2) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(8P23.2) MUTATED   126  81
  DEL PEAK 23(8P23.2) WILD-TYPE 228 164
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                          207                           392 
  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                           81                           164 
$`DEL PEAK 23(8P23.2) MUTATED`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE 
       15.68        60.39        34.85        18.28         4.31        24.00 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-2H-A9GF TCGA-2H-A9GH 
       27.12         5.16        47.05        22.98        25.78        31.27 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 
        5.92        13.94         4.21         0.85         2.63        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS 
        3.88         0.53        17.03         0.79        23.41         9.96 
TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       14.50        44.75         3.68        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OT 
       25.22        24.03        26.33        32.61         3.32         4.90 
TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF 
        7.43         2.60        25.12         7.40         3.75         2.66 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ 
       13.22         5.49         8.71        13.41        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y 
       10.45        12.66        12.43        13.15        13.25        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.49        12.76        22.39        12.33        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.33        25.25        12.00        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6Y0 
       12.03        12.85        12.26         7.82         8.02        53.95 
TCGA-R6-A8WC TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV 
        2.30        20.38         5.29         3.42        16.44        15.35 
TCGA-V5-AASW TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
        9.27        12.43        18.31         8.12        28.11        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-A5TI 
       41.23         2.10         1.32         2.66        58.03        19.56 
TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6705 
        9.44        18.35        17.29        13.68         9.17        25.61 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7958 
       12.16         9.21        33.63        39.78        28.73        29.56 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8362 
        0.69         9.60        29.42         2.66        15.58        13.08 
TCGA-BR-8485 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U 
        9.21        31.96        32.58         9.86         8.22        13.87 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       12.89         0.72        13.51        20.65         1.15        21.44 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 
       13.15        13.35        12.10        12.53         7.17        15.39 
TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 
        6.31        12.43        11.61        12.20         3.02         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5724 
       54.08         4.01        29.98        19.07        36.00        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 
       15.02         4.01        69.04        12.66        19.13        18.54 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6F2 
       17.19        15.22        11.31        24.72        16.44        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8099 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 
       19.96         0.62        17.06        63.06         5.92        18.15 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-8663 
       28.96         0.76        22.75         6.58        33.40         3.39 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 
        6.44         6.74         6.51        11.70        15.75         2.53 
TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A805 
        5.56        36.95        14.04        45.67         8.52         9.24 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E0 
        8.61       122.30        37.91         5.79         0.92        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       43.36        37.41         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A91Z 
       17.85         1.87        13.35        39.45         1.71        55.56 
TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        4.54        11.24        18.41        43.66        32.94        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        27.55        12.43 

$`DEL PEAK 23(8P23.2) WILD-TYPE`
TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
        8.94         4.70        19.99        22.82         0.36        35.97 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       20.02        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
        9.86        27.35        26.93        14.30        58.55         7.63 
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        35.21 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       20.78        20.12         9.30        12.82        14.86         4.67 
TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC 
       12.16       122.10        68.02        41.52        21.70         6.28 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25         0.30        21.01        47.93        18.35 
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-A88S TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
       15.48         3.02        55.50        12.92        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.55         7.76        21.37        83.24        52.57        46.09 
TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49V 
        5.92        13.41        12.33        13.38        15.35        12.59 
TCGA-LN-A49X TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 
       12.62        12.59        12.85        15.52        11.54         4.47 
TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-M9-A5M8 
       10.52        12.23        12.03        13.18        13.38        33.11 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.59         5.06        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-AASX 
        9.30        15.78         2.89        12.69         7.00         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EZ TCGA-VR-AA4D 
       25.81        27.09        22.82         1.55        18.18        46.19 
TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       18.21        14.37         3.42        19.73        26.70        11.70 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
       30.90         4.08         4.08         9.34         9.67         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 
        9.57         6.61        34.68        15.95        13.87        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       39.12        26.10        32.78        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       35.24        35.84        18.15        15.32         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       33.21        37.25        14.43        11.44        29.59        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
        8.05         0.56        19.96         2.20         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       31.10         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         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        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
        7.53        26.73        24.79        20.88        10.68        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        7.53         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.18        11.21        12.76        12.59        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.39        12.59        11.64        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.30        11.31         6.58        11.77        12.62        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4455 
       27.02        15.95         1.02         8.05        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       28.96        65.10        21.07         7.99        25.71        20.91 
TCGA-D7-6519 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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       15.98        12.79        12.36        12.33        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-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       13.58         0.56         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       30.51        26.47         1.51        24.39        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-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        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       29.00        23.84        23.80        21.17        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H 
       19.53        12.59        10.62        13.51        63.62        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        3.72        19.73        18.21        74.53         6.08         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13        16.67        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-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       48.79         5.46        13.25        13.02        21.73        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       37.22        30.97        34.29        16.31         2.50         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       73.41        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
       32.88        42.64        60.85         9.50         9.73         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        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G 
        2.66        42.54        28.41        38.93        17.13        26.04 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE 
                         0.13                          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 
                        13.18                         14.45 
[1] "0.1 - 122.3 (13.2)" "0.0 - 122.1 (14.4)"
[1] "hr=" "1"  
D61V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(8P23.2) MUTATED         3        5        9        9        32
  DEL PEAK 23(8P23.2) WILD-TYPE       7       16       38       24        55
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(8P23.2) MUTATED          33        13         28         32
  DEL PEAK 23(8P23.2) WILD-TYPE        54        15         67         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 23(8P23.2) MUTATED           16       19         2
  DEL PEAK 23(8P23.2) WILD-TYPE         30       30         2
D61V3, multiclass
            clus
vv           DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                             5                            16
  STAGE IB                             9                            38
  STAGE II                             9                            24
  STAGE IIA                           32                            55
  STAGE IIB                           33                            54
  STAGE III                           13                            15
  STAGE IIIA                          28                            67
  STAGE IIIB                          32                            40
  STAGE IIIC                          16                            30
  STAGE IV                            19                            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 23(8P23.2) MUTATED      19  43 112  32
  DEL PEAK 23(8P23.2) WILD-TYPE    36  93 171  92
D61V4, multiclass
       clus
vv      DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  T0+T1                          19                            36
  T2                             43                            93
  T3                            112                           171
  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    64  67  34  38
  DEL PEAK 23(8P23.2) WILD-TYPE 143 120  64  58
D61V5, multiclass
    clus
vv   DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  N0                          64                           143
  N1                          67                           120
  N2                          34                            64
  N3                          38                            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"
D61V6, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED   177  16
  DEL PEAK 23(8P23.2) WILD-TYPE 347  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED    177   16
  DEL PEAK 23(8P23.2) WILD-TYPE  347   23
   clus
vv  DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  0                         177                           347
  1                          16                            23
[1] 2 2
[1] FALSE
D61V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED    44 170
  DEL PEAK 23(8P23.2) WILD-TYPE 141 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED     44  170
  DEL PEAK 23(8P23.2) WILD-TYPE  141  270
        clus
vv       DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  FEMALE                          44                           141
  MALE                           170                           270
[1] 2 2
[1] FALSE
D61V8, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED   145  49
  DEL PEAK 23(8P23.2) WILD-TYPE 300  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED    145   49
  DEL PEAK 23(8P23.2) WILD-TYPE  300   70
     clus
vv    DEL PEAK 23(8P23.2) MUTATED DEL PEAK 23(8P23.2) WILD-TYPE
  NO                          145                           300
  YES                          49                            70
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(8P23.2) MUTATED      51                         8
  DEL PEAK 23(8P23.2) WILD-TYPE    83                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 23(8P23.2) MUTATED                                           1   126
  DEL PEAK 23(8P23.2) WILD-TYPE                                         0   266
D61V11, multiclass
                                           clus
vv                                          DEL PEAK 23(8P23.2) MUTATED
  ASIAN                                                              51
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             126
                                           clus
vv                                          DEL PEAK 23(8P23.2) WILD-TYPE
  ASIAN                                                                83
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               266
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 23(8P23.2) MUTATED     5 125
  DEL PEAK 23(8P23.2) WILD-TYPE   6 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(8P23.2) MUTATED      5  125
  DEL PEAK 23(8P23.2) WILD-TYPE    6  279
                        clus
vv                       DEL PEAK 23(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         125
                        clus
vv                       DEL PEAK 23(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 24(9P23) MUTATION ANALYSIS
D62V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 24(9P23) MUTATED   174 119
  DEL PEAK 24(9P23) WILD-TYPE 180 126
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        293                         306 
  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                        119                         126 
$`DEL PEAK 24(9P23) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-Q9-A6FU 
       60.39        34.85        18.28         8.94        35.97         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.02        47.05        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ 
       14.30         7.63        13.94         8.94        16.24         4.21 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       32.45         7.69        20.12        18.64         3.88         0.53 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
        0.79        23.41         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       68.02        25.22         3.16         0.30        26.33        32.61 
TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
       18.35         3.32         7.17         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43        15.48         2.60         3.75        55.50         2.66 
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-A49P TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.66        12.33        13.38        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.76        22.39        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       15.52        12.33        13.22        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP 
       12.00        12.23        12.03        12.33         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
       12.26        33.11         5.06        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
       15.78         2.30        12.69        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
       16.44         9.27         8.98        25.81        27.09        22.82 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 
       12.43         1.55        18.31         8.12        28.11        52.27 
TCGA-VR-AA4D TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       46.19        18.21        41.23        14.37         3.42         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        58.03        26.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4257 
        9.44         6.61        18.35         4.08         4.08         9.67 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6803 
       17.29        13.68        19.33        19.89        12.16        31.20 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.24        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       28.73         3.45        33.21        37.25        11.44         0.69 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
        8.05         2.66        19.96        22.19        17.52        14.04 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8676 TCGA-BR-8682 
        5.39        25.18         9.21        20.22         7.53        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88         8.22        13.87        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
        0.72         0.66        13.51        20.65         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       13.02        13.15        11.21        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 
        7.17        12.39        11.64        15.39        12.07         6.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.43        11.61         3.02         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 
       29.98        19.07        12.03        18.97        12.00        36.00 
TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 
        1.02       105.07        12.03         4.01        69.04        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        20.91        19.13        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       13.35        17.19        10.26        15.98        12.79        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV 
       19.50        18.21        14.66        21.14        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C 
       11.31        22.29        15.65        19.96         7.99        11.38 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       19.53        14.07        17.06         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GF TCGA-HU-A4GH 
       63.06         1.51         5.92        18.15        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        6.58        29.00        21.17        33.40        36.36        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38        12.46        13.35         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H 
        6.51        10.62        15.75        13.51         5.56        37.64 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       36.95        14.04        45.67         8.52         6.08         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
        8.61         5.13        16.67       122.30        37.91       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        8.94         5.79        48.79        13.25        18.48        43.36 
TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       37.41         7.73        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q 
       17.85         1.87        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        42.64         9.50         9.73        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        2.01        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       38.93        54.12        27.55        12.43         0.79 

$`DEL PEAK 24(9P23) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NT TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        0.36        27.12        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-IG-A3I8 
        0.23        20.15         9.86        58.55         5.92        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D 
       35.21         0.85        20.78         2.63         9.30        17.03 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       12.82         9.96        14.86       122.10         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OU 
       30.25        21.01        47.93         1.38         4.90        29.00 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK 
       25.12         7.40         3.02        12.92        13.48        13.55 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        7.76         5.49        21.37        52.57        46.09        10.85 
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        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.59        11.54         4.47        13.18        13.38        13.18 
TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EY TCGA-VR-A8EZ 
       53.95         2.89         7.00        15.35        33.70        18.18 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-Z6-A8JE 
       18.05        11.24         9.17        15.91        25.08         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-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-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-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       18.05         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 
       36.16        35.84         9.07        29.56        14.43        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 
        9.60        32.25         0.56        29.42         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        31.10        13.08         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34        28.14         6.28        26.73        24.79        31.96 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        34.13         7.53         6.08        27.55        28.57 
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        28.34        32.52 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        20.42        16.14         5.13        13.41        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 
       13.35        12.76        12.33        12.30        12.59        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43        12.30        11.31         6.58        12.20        11.77 
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-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       14.01         0.00         9.01         7.07        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99        15.02        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 
       21.07         7.99        18.61        17.85        15.22        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT 
       12.33        24.72        16.80        17.19        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        26.43        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
       20.32         8.38         4.34         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       72.23        21.27         3.48        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 
       13.58        77.29        52.21        30.51        26.47        24.39 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       28.96        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        0.26         2.10        12.95        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IP-7968 
       15.68         3.45         3.39        19.53        11.70         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 
       63.62         3.72        19.73        18.21        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       11.05        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 
       16.87        19.04         0.92         5.46        13.02        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        9.27        23.41        15.65        13.35        29.59        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       39.45        11.70        21.83        61.22        32.88        60.85 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZA-A8F6 
       28.41        32.94        17.13        26.04        16.14        17.26 

  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE 
                       0.13                        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 
                     13.350                      14.775 
[1] "0.1 - 122.3 (13.3)" "0.0 - 122.1 (14.8)"
[1] "hr=" "1.1"
D62V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P23) MUTATED         3       10       14       18        46
  DEL PEAK 24(9P23) WILD-TYPE       7       11       33       15        41
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P23) MUTATED          44        19         44         33
  DEL PEAK 24(9P23) WILD-TYPE        43         9         51         39
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(9P23) MUTATED           19       22         4
  DEL PEAK 24(9P23) WILD-TYPE         27       27         0
D62V3, multiclass
            clus
vv           DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  STAGE I                            3                           7
  STAGE IA                          10                          11
  STAGE IB                          14                          33
  STAGE II                          18                          15
  STAGE IIA                         46                          41
  STAGE IIB                         44                          43
  STAGE III                         19                           9
  STAGE IIIA                        44                          51
  STAGE IIIB                        33                          39
  STAGE IIIC                        19                          27
  STAGE IV                          22                          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 24(9P23) MUTATED      28  65 148  46
  DEL PEAK 24(9P23) WILD-TYPE    27  71 135  78
D62V4, multiclass
       clus
vv      DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  T0+T1                        28                          27
  T2                           65                          71
  T3                          148                         135
  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    90 102  48  43
  DEL PEAK 24(9P23) WILD-TYPE 117  85  50  53
D62V5, multiclass
    clus
vv   DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  N0                        90                         117
  N1                       102                          85
  N2                        48                          50
  N3                        43                          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"
D62V6, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED   255  16
  DEL PEAK 24(9P23) WILD-TYPE 269  23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED    255   16
  DEL PEAK 24(9P23) WILD-TYPE  269   23
   clus
vv  DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  0                       255                         269
  1                        16                          23
[1] 2 2
[1] FALSE
D62V7, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED    77 225
  DEL PEAK 24(9P23) WILD-TYPE 108 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED     77  225
  DEL PEAK 24(9P23) WILD-TYPE  108  215
        clus
vv       DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  FEMALE                        77                         108
  MALE                         225                         215
[1] 2 2
[1] FALSE
D62V8, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED   210  64
  DEL PEAK 24(9P23) WILD-TYPE 235  55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED    210   64
  DEL PEAK 24(9P23) WILD-TYPE  235   55
     clus
vv    DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  NO                        210                         235
  YES                        64                          55
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(9P23) MUTATED      65                         7
  DEL PEAK 24(9P23) WILD-TYPE    69                        10
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 24(9P23) MUTATED                                           1   184
  DEL PEAK 24(9P23) WILD-TYPE                                         0   208
D62V11, multiclass
                                           clus
vv                                          DEL PEAK 24(9P23) MUTATED
  ASIAN                                                            65
  BLACK OR AFRICAN AMERICAN                                         7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           184
                                           clus
vv                                          DEL PEAK 24(9P23) WILD-TYPE
  ASIAN                                                              69
  BLACK OR AFRICAN AMERICAN                                          10
  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"
D62V12, binary
                             cls
clus                            0   1
  DEL PEAK 24(9P23) MUTATED     7 189
  DEL PEAK 24(9P23) WILD-TYPE   4 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(9P23) MUTATED      7  189
  DEL PEAK 24(9P23) WILD-TYPE    4  215
                        clus
vv                       DEL PEAK 24(9P23) MUTATED DEL PEAK 24(9P23) WILD-TYPE
  HISPANIC OR LATINO                             7                           4
  NOT HISPANIC OR LATINO                       189                         215
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 25(9P21.3) MUTATION ANALYSIS
D63V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 25(9P21.3) MUTATED   194 133
  DEL PEAK 25(9P21.3) WILD-TYPE 160 112
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          327                           272 
  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                          133                           112 
$`DEL PEAK 25(9P21.3) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A88Y 
       60.39        34.85        18.28         4.31         8.94         0.36 
TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-VQ-A8PU TCGA-VQ-A94U 
       35.97         5.16        20.02        47.05        27.35        26.93 
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-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H 
       12.16        44.75        23.18        25.22         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
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        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         3.75         3.02        55.50         2.66        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-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       13.41        83.24        10.85        10.36         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        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        12.85        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.00        12.23        12.03        13.18        12.33        13.38 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
        0.13        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        5.06        16.31        38.40         6.35         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        9.27         8.98        25.81        22.82        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
       18.31         8.12        28.11        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 
       58.03        19.56        11.01         9.44         6.61        18.35 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6709 
        4.08         9.67        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        33.63        39.78        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        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 
       11.44         0.69        19.96        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        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88         8.22        13.87        34.98         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 
       21.44        13.41        13.02        13.15        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
       12.59        12.53         7.17        12.39        11.64        15.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4304 
       12.07         6.31        12.43        11.61         3.02        27.02 
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-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        20.91 
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        22.29        19.96 
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-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        6.21        63.06         1.51         5.92        24.39        18.15 
TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
        5.59        11.77         6.58        23.80        21.17        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS 
       36.36        18.81        12.46        13.35         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
       63.62        37.64        36.95        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
        6.08         9.24         8.61         5.13        16.67        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
      115.69         8.94         5.79        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        21.73        37.41        37.22         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       46.26        22.19        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V 
       64.57        14.33        18.74        20.81         1.71        42.64 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.50         9.73        55.56         9.04        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6J 
       11.24        18.41        43.66        38.93        54.12        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

$`DEL PEAK 25(9P21.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT 
       15.68        24.00         4.70        19.99        22.82        27.12 
TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       21.99        22.98        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3QL TCGA-IG-A4QT 
        9.86        58.55         5.92        13.94        35.21         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        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OJ 
       21.70        31.56        24.03         6.28        30.25        21.01 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NI TCGA-L5-A8NM 
        1.38         3.16        25.12         7.40        13.48         7.76 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A8I1 TCGA-R6-A6DN TCGA-R6-A6DQ 
       52.57        46.09        12.59        13.18         8.02         7.59 
TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-AASV TCGA-VR-A8EP 
        7.04        53.95         2.89         7.00        15.35        27.09 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 
       33.70        52.27        26.70        11.70         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
        4.64         7.43        30.90         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.87        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
        8.98        40.21        30.90        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       35.84         9.07        29.56        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        31.10        13.08         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        24.79        31.96 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        34.13         7.53         6.08        27.55        28.57 
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        28.34        32.52 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 
        0.46        16.14         5.13        13.18        13.35        12.10 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
       12.33        12.30        12.59        12.82        12.43        12.30 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-4465 
       15.95         1.02         7.99         8.05         0.00         9.01 
TCGA-CG-4469 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        7.07         6.97         6.02         0.99       105.07        28.96 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 
       65.10        21.07         7.99        25.71        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.85        15.22        12.36        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       19.50        17.19        20.91         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 
       14.76        26.43        11.44        20.32        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13         0.62        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-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 
       77.29        52.21        30.51        26.47        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       12.95        29.00        23.84        14.07        15.68         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU TCGA-MX-A5UG 
        3.39        18.38        19.53         6.44        11.70         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV 
       19.73        18.21        74.53         4.60        11.05       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-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       19.04         0.92         5.46        38.14        30.97        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-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       32.88        60.85         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
        5.72        66.81         2.66        28.41        32.94        17.13 
TCGA-VQ-AA6G TCGA-VQ-AA6I 
       26.04        16.14 

  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE 
                         0.13                          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 
                       13.350                        15.665 
[1] "0.1 - 115.7 (13.3)" "0.0 - 122.3 (15.7)"
[1] "hr=" "1.1"
D63V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9P21.3) MUTATED         3       12       21       18        54
  DEL PEAK 25(9P21.3) WILD-TYPE       7        9       26       15        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9P21.3) MUTATED          48        23         47         34
  DEL PEAK 25(9P21.3) WILD-TYPE        39         5         48         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(9P21.3) MUTATED           18       26         4
  DEL PEAK 25(9P21.3) WILD-TYPE         28       23         0
D63V3, multiclass
            clus
vv           DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  STAGE I                              3                             7
  STAGE IA                            12                             9
  STAGE IB                            21                            26
  STAGE II                            18                            15
  STAGE IIA                           54                            33
  STAGE IIB                           48                            39
  STAGE III                           23                             5
  STAGE IIIA                          47                            48
  STAGE IIIB                          34                            38
  STAGE IIIC                          18                            28
  STAGE IV                            26                            23
  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      31  78 162  47
  DEL PEAK 25(9P21.3) WILD-TYPE    24  58 121  77
D63V4, multiclass
       clus
vv      DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  T0+T1                          31                            24
  T2                             78                            58
  T3                            162                           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   113 109  52  41
  DEL PEAK 25(9P21.3) WILD-TYPE  94  78  46  55
D63V5, multiclass
    clus
vv   DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  N0                         113                            94
  N1                         109                            78
  N2                          52                            46
  N3                          41                            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"
D63V6, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED   276  20
  DEL PEAK 25(9P21.3) WILD-TYPE 248  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED    276   20
  DEL PEAK 25(9P21.3) WILD-TYPE  248   19
   clus
vv  DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  0                         276                           248
  1                          20                            19
[1] 2 2
[1] FALSE
D63V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED    82 252
  DEL PEAK 25(9P21.3) WILD-TYPE 103 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED     82  252
  DEL PEAK 25(9P21.3) WILD-TYPE  103  188
        clus
vv       DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  FEMALE                          82                           103
  MALE                           252                           188
[1] 2 2
[1] FALSE
D63V8, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED   228  72
  DEL PEAK 25(9P21.3) WILD-TYPE 217  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED    228   72
  DEL PEAK 25(9P21.3) WILD-TYPE  217   47
     clus
vv    DEL PEAK 25(9P21.3) MUTATED DEL PEAK 25(9P21.3) WILD-TYPE
  NO                          228                           217
  YES                          72                            47
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(9P21.3) MUTATED      77                        11
  DEL PEAK 25(9P21.3) WILD-TYPE    57                         6
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 25(9P21.3) MUTATED                                           1   197
  DEL PEAK 25(9P21.3) WILD-TYPE                                         0   195
D63V11, multiclass
                                           clus
vv                                          DEL PEAK 25(9P21.3) MUTATED
  ASIAN                                                              77
  BLACK OR AFRICAN AMERICAN                                          11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             197
                                           clus
vv                                          DEL PEAK 25(9P21.3) WILD-TYPE
  ASIAN                                                                57
  BLACK OR AFRICAN AMERICAN                                             6
  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"
D63V12, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.3) MUTATED     8 203
  DEL PEAK 25(9P21.3) WILD-TYPE   3 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.3) MUTATED      8  203
  DEL PEAK 25(9P21.3) WILD-TYPE    3  201
                        clus
vv                       DEL PEAK 25(9P21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         203
                        clus
vv                       DEL PEAK 25(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           201
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 26(9Q21.11) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(9Q21.11) MUTATED    92  78
  DEL PEAK 26(9Q21.11) WILD-TYPE 262 167
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           170                            429 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                            78                            167 
$`DEL PEAK 26(9Q21.11) MUTATED`
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A8NG TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       18.28         8.94        35.97        26.93        25.78        31.27 
TCGA-2H-A9GO TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A5B8 
       16.24         0.85        20.78        20.12         3.88         0.79 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF 
       23.41         4.67        44.75        25.22         0.30        26.33 
TCGA-L5-A4OM TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A8NE TCGA-L5-A8NF 
       47.93        58.59         7.13        15.48        55.50         2.66 
TCGA-L5-A8NS TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49R 
       13.41        46.09        10.85         5.92        12.66        13.38 
TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A6 
       13.15        13.25        12.46        12.59        12.76        12.85 
TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.33        12.00        12.23        12.33        13.18         0.13 
TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC 
        5.06        38.40         6.35         9.30        15.78         2.30 
TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ET 
       12.69         3.42        16.44        25.81        27.09         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR 
        8.12        28.11        18.18        52.27        11.24        18.21 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        3.42         2.10        19.73        11.01         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 
        4.08         9.67        17.29        13.68        19.33        31.20 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 
       33.63        39.78        18.15        28.73         3.45        37.25 
TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       19.96        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 
       32.58        20.88         8.22        34.98         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        21.44        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
       11.21        12.59         7.17        11.64        15.39         6.31 
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        22.29 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 
       19.96         7.99        72.23        11.38        17.06        13.58 
TCGA-FP-8631 TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GF 
        0.56        63.06         5.92        18.15        28.96        25.81 
TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-IN-A6RI TCGA-IN-A6RJ 
       11.77         6.58         2.10        21.17        18.38        12.46 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93H TCGA-MX-A666 
        6.44         6.74         6.51        15.75        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
       45.67         8.52         6.08        16.67        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.79        13.25        18.48        43.36        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Y 
        2.70        17.85        13.35        20.81        42.64         9.73 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A 
        9.04        21.04        42.54        11.24        43.66        38.93 
TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       27.55         0.79 

$`DEL PEAK 26(9Q21.11) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        34.85         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       20.15         9.86        27.35        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94         8.94         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L 
       33.27        35.21         2.63        18.64         9.30         0.53 
TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I 
       17.03        12.82         9.96        14.86        14.50        12.16 
TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 
      122.10        68.02         3.68        41.52        47.38        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-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ 
       32.61        21.01        18.35         3.32         7.17         1.38 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        3.16         4.90        29.00         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.40         3.75         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-A8NU TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O 
       83.24        52.57        10.36        10.45        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 TCGA-LN-A4A4 
       12.33        15.35        12.59        12.62        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-LN-A8I0 TCGA-LN-A9FP 
       25.25        10.52        12.03        13.18        13.38        12.03 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.85        12.26        33.11         7.82         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW 
       16.31         7.04        53.95         2.89         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ER 
        5.29        15.35         9.27         8.98        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31        33.70        46.19        18.05         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 
       25.08        41.23        14.37         1.32         2.66        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 
        9.57         6.61        34.68        15.95        13.87        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-6852 TCGA-BR-7196 
       12.16         8.98        40.21        30.90        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 
        9.21        36.16        35.24        35.84        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.26         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        31.96         9.86 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       10.68        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
        0.66        32.52         0.46        20.65        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
        5.13        13.41        13.18        12.10        12.76        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-8535 
       12.33        12.30        12.39        12.59        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        12.43         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        19.07         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-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-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-D7-6522 TCGA-D7-6524 
       25.71        12.66        20.91        19.13        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19        15.22        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        19.50        17.19        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.31        11.44        20.32        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         0.62        14.47        21.27         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM 
       14.07        22.29        59.54         5.03         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       22.32        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ 
       24.26        22.68        24.20         3.25        22.75        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL 
       33.40        36.36         3.45        18.81         3.39        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
       19.53        12.59        10.62        11.70        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE 
        5.56        63.62        36.95         3.72        19.73        18.21 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         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        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM 
       30.97        34.29        46.26        16.31         2.50         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        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A923 
       32.88         1.71        60.85         9.50        55.56         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        66.81         2.66 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        12.43        17.26 

  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                          0.13                           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 
                        13.395                         14.070 
[1] "0.1 - 72.2 (13.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(9Q21.11) MUTATED         1        5       10       10        26
  DEL PEAK 26(9Q21.11) WILD-TYPE       9       16       37       23        61
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(9Q21.11) MUTATED          25         7         27         18
  DEL PEAK 26(9Q21.11) WILD-TYPE        62        21         68         54
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 26(9Q21.11) MUTATED           15       11         4
  DEL PEAK 26(9Q21.11) WILD-TYPE         31       38         0
D64V3, multiclass
            clus
vv           DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              5                             16
  STAGE IB                             10                             37
  STAGE II                             10                             23
  STAGE IIA                            26                             61
  STAGE IIB                            25                             62
  STAGE III                             7                             21
  STAGE IIIA                           27                             68
  STAGE IIIB                           18                             54
  STAGE IIIC                           15                             31
  STAGE IV                             11                             38
  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  33  88  31
  DEL PEAK 26(9Q21.11) WILD-TYPE    43 103 195  93
D64V4, multiclass
       clus
vv      DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  T0+T1                           12                             43
  T2                              33                            103
  T3                              88                            195
  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    54  52  30  25
  DEL PEAK 26(9Q21.11) WILD-TYPE 153 135  68  71
D64V5, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  N0                           54                            153
  N1                           52                            135
  N2                           30                             68
  N3                           25                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED   144  10
  DEL PEAK 26(9Q21.11) WILD-TYPE 380  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED    144   10
  DEL PEAK 26(9Q21.11) WILD-TYPE  380   29
   clus
vv  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  0                          144                            380
  1                           10                             29
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED    43 132
  DEL PEAK 26(9Q21.11) WILD-TYPE 142 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED     43  132
  DEL PEAK 26(9Q21.11) WILD-TYPE  142  308
        clus
vv       DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  FEMALE                           43                            142
  MALE                            132                            308
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED   131  34
  DEL PEAK 26(9Q21.11) WILD-TYPE 314  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED    131   34
  DEL PEAK 26(9Q21.11) WILD-TYPE  314   85
     clus
vv    DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  NO                           131                            314
  YES                           34                             85
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(9Q21.11) MUTATED      44                         8
  DEL PEAK 26(9Q21.11) WILD-TYPE    90                         9
                                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     106
  DEL PEAK 26(9Q21.11) WILD-TYPE   286
D64V11, multiclass
                                           clus
vv                                          DEL PEAK 26(9Q21.11) MUTATED
  ASIAN                                                               44
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              106
                                           clus
vv                                          DEL PEAK 26(9Q21.11) WILD-TYPE
  ASIAN                                                                 90
  BLACK OR AFRICAN AMERICAN                                              9
  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"
D64V12, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     3 119
  DEL PEAK 26(9Q21.11) WILD-TYPE   8 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      3  119
  DEL PEAK 26(9Q21.11) WILD-TYPE    8  285
                        clus
vv                       DEL PEAK 26(9Q21.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 26(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            285
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 27(10P15.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.3) MUTATED    67  60
  DEL PEAK 27(10P15.3) WILD-TYPE 287 185
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           127                            472 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                            60                            185 
$`DEL PEAK 27(10P15.3) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-CG-4475 
        4.31         8.94        24.00         4.70        27.12        22.98 
TCGA-FP-A8CX TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 
        0.23        25.78        14.30         5.92         4.21        33.27 
TCGA-IG-A3Y9 TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
        0.85        18.64         0.53         0.79        23.41        14.50 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A88V 
       23.18         0.30         3.32         3.16         4.90         2.60 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49O TCGA-LN-A49W 
       13.41        83.24        10.85         5.92        13.41        13.25 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 
       22.39        11.54        12.33        13.22         4.47        25.25 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ 
       12.03        13.18        12.33        13.38         0.13        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
       12.26         7.82        53.95         5.29         3.42        16.44 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-XP-A8T6 TCGA-XP-A8T8 
        8.12        18.18        18.05        11.24        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4191 TCGA-BR-4255 
        3.42         2.66        19.56        11.01        18.35         4.08 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 
        9.67         6.18        19.33        26.10         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
       11.44        19.96        17.52        20.22        24.79         9.86 
TCGA-BR-A452 TCGA-BR-A4IY TCGA-BR-A4J7 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        7.53        12.89        32.52        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A487 TCGA-CG-4301 TCGA-CG-4441 TCGA-CG-4455 
       12.30        15.39        12.30         3.02        14.01        12.03 
TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8570 
       69.04        18.54        15.22        15.98        11.31        24.72 
TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       18.21        14.27        11.24         7.99        19.53         0.56 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GU TCGA-IN-8462 
        5.52        63.06         5.92        28.96         6.58        18.81 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-R5-A7ZF TCGA-R5-A805 TCGA-RD-A8N1 TCGA-RD-A8N6 
        6.44         6.74         8.52         9.24       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        5.79         0.92        48.79        13.02        18.48        43.36 
TCGA-VQ-A8P3 TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 
       37.22        13.35        18.74        20.81         9.04         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6I 
        5.72        66.81        11.24        18.41        43.66        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 27(10P15.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
        0.36        35.97         5.16        20.02        47.05        21.99 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07        16.24        20.15         9.86        27.35        26.93 
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-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
       32.45         7.69        35.21        20.78         2.63        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP 
        3.88         9.30        17.03        12.82         9.96        14.86 
TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        12.16       122.10        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
       47.93        18.35         7.17         1.38        58.59        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43        15.48        25.12         7.40         3.75 
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-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.55        13.22         7.76         5.49        21.37         8.71 
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-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
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        12.85 
TCGA-LN-A4A8 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8I1 
       15.52        12.33        10.52        12.00        12.23        13.18 
TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.03        33.11         8.02         7.59         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04        38.40         6.35         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASW 
        2.30        12.69         7.00        20.38        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
        8.98        25.81        27.09        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        33.70        52.27        46.19         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       15.91        18.21        41.23         2.10         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       58.03        26.70        11.70         9.47         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        6.97         4.64         7.43        30.90         4.08         9.34 
TCGA-BR-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-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       44.94        21.90         9.21        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       33.63        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       29.56        33.21        37.25         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
       32.25         8.05         0.56        29.42         2.66         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        6.08        34.98         1.48        27.55        28.57         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72        14.17         0.53        28.34         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        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 
       11.21        12.10        12.76        12.53        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
       11.64        12.07        12.82        12.43         6.31        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        11.61         6.58        12.20        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-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-4449 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        29.98        19.07         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-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       25.71        12.66        20.91        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        10.26        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       12.36        12.33        16.80        19.50        17.19        14.66 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.31        11.44        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       15.65         8.38         4.34        19.96         7.13         0.62 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03        13.58         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       77.29        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        20.25         0.26         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       19.53        12.59         6.51        10.62        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       13.51         2.53         5.56        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
        3.72        19.73        14.04        45.67        18.21        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-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-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-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E3 
       35.61        16.87        19.04         5.46        13.25        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94O TCGA-VQ-A94P 
       55.56         2.01        55.43         6.58        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        27.55        12.43        17.26 

  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                          0.13                           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 
                        12.590                         14.825 
[1] "0.1 - 115.7 (12.6)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.5"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10P15.3) MUTATED         1        3        6        3        17
  DEL PEAK 27(10P15.3) WILD-TYPE       9       18       41       30        70
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10P15.3) MUTATED          25        10         21         13
  DEL PEAK 27(10P15.3) WILD-TYPE        62        18         74         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         37       36         4
D65V3, multiclass
            clus
vv           DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              3                             18
  STAGE IB                              6                             41
  STAGE II                              3                             30
  STAGE IIA                            17                             70
  STAGE IIB                            25                             62
  STAGE III                            10                             18
  STAGE IIIA                           21                             74
  STAGE IIIB                           13                             59
  STAGE IIIC                            9                             37
  STAGE IV                             13                             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
  DEL PEAK 27(10P15.3) MUTATED       8  30  65  21
  DEL PEAK 27(10P15.3) WILD-TYPE    47 106 218 103
D65V4, multiclass
       clus
vv      DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  T0+T1                            8                             47
  T2                              30                            106
  T3                              65                            218
  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    36  40  26  20
  DEL PEAK 27(10P15.3) WILD-TYPE 171 147  72  76
D65V5, multiclass
    clus
vv   DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  N0                           36                            171
  N1                           40                            147
  N2                           26                             72
  N3                           20                             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"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED   111   7
  DEL PEAK 27(10P15.3) WILD-TYPE 413  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED    111    7
  DEL PEAK 27(10P15.3) WILD-TYPE  413   32
   clus
vv  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  0                          111                            413
  1                            7                             32
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED    29 102
  DEL PEAK 27(10P15.3) WILD-TYPE 156 338
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     29  102
  DEL PEAK 27(10P15.3) WILD-TYPE  156  338
        clus
vv       DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  FEMALE                           29                            156
  MALE                            102                            338
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED    92  27
  DEL PEAK 27(10P15.3) WILD-TYPE 353  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     92   27
  DEL PEAK 27(10P15.3) WILD-TYPE  353   92
     clus
vv    DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  NO                            92                            353
  YES                           27                             92
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(10P15.3) MUTATED      35                         7
  DEL PEAK 27(10P15.3) WILD-TYPE    99                        10
                                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   320
D65V11, multiclass
                                           clus
vv                                          DEL PEAK 27(10P15.3) MUTATED
  ASIAN                                                               35
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               72
                                           clus
vv                                          DEL PEAK 27(10P15.3) WILD-TYPE
  ASIAN                                                                 99
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                320
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED     3  83
  DEL PEAK 27(10P15.3) WILD-TYPE   8 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED      3   83
  DEL PEAK 27(10P15.3) WILD-TYPE    8  321
                        clus
vv                       DEL PEAK 27(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           83
                        clus
vv                       DEL PEAK 27(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            321
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 28(10P11.21) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10P11.21) MUTATED    53  45
  DEL PEAK 28(10P11.21) WILD-TYPE 301 200
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             98                             501 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             45                             200 
$`DEL PEAK 28(10P11.21) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-CG-4475 TCGA-2H-A9GI 
        4.31        24.00         4.70        27.12        22.98        14.30 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 
        5.92        13.94        33.27         0.85        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FE 
        0.53         0.79        23.41        14.50        44.75         3.68 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OT TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NU 
       23.18         0.30         4.90        13.48        13.55        83.24 
TCGA-L7-A56G TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A1 
       10.85        13.41        13.15        12.59        13.25        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV 
       22.39        11.54        13.22         4.47        25.25        10.52 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR 
       13.18        12.33        13.38         0.13        12.85        12.26 
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        18.05        11.24 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-BR-4257 
       25.08        41.23        14.37         3.42         2.66         9.67 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8291 
       19.33        26.10         3.45        14.43        11.44        19.96 
TCGA-BR-8365 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A4MH 
       17.52        12.59         7.17        12.33        15.39        12.20 
TCGA-CG-4455 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       12.03        69.04        18.54        15.98        12.79        11.31 
TCGA-D7-8575 TCGA-D7-A6F0 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 
       18.21        22.29        19.53         0.56         5.52        63.06 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-8462 TCGA-IN-A6RP TCGA-R5-A7ZF 
       28.96        22.82        23.80        18.81         6.44         8.52 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E0 
      115.69         8.94         5.79        48.79        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-A94T 
       43.36        13.35        18.74        20.81         5.72        11.24 
TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       43.66         0.79 

$`DEL PEAK 28(10P11.21) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 
       22.82         0.36        35.97         5.16        20.02        47.05 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        79.07        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.35        26.93        25.78        31.27        58.55         7.63 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3QL 
        8.94        16.24         4.21        32.45         7.69        35.21 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       20.78         2.63         3.88         9.30        17.03        12.82 
TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
        9.96        14.86         4.67        12.16       122.10        68.02 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
        6.28         3.16        30.25        26.33        32.61        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-A4OS TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
       58.59        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
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-A49P TCGA-LN-A49R TCGA-LN-A49U 
       10.45        12.66        12.43        12.33        13.38        15.35 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       12.62        12.46        12.49        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       15.52        12.33        12.33        12.00        12.23        12.03 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       13.18        12.03        33.11         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        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        9.30        15.78         2.89         2.30        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX 
       20.38         5.29        16.44        15.35         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
       25.81        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       33.70        52.27        46.19         9.17        15.91        18.21 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 
        2.10         1.32        19.73        58.03        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.87        17.29        13.68        39.12         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 
       28.73         9.07        29.56        33.21        37.25         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       29.59         9.60        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        2.66         2.20        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
       13.08         0.26        22.19         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        6.08        34.98         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       21.44        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 
       13.18        13.35        11.21        12.10        12.76        12.53 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 
       12.30        12.39        12.59        11.64        12.07        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.43         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        6.58        11.77        12.62        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10         4.01        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        20.91        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 
       17.85        13.35        17.19        10.26        15.22        12.36 
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        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        26.43        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       20.32        15.65         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        0.62         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        3.48        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
        1.51         5.92        24.39        18.15        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.74        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       45.67        18.21        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-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-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       19.04         0.92         5.46        13.25        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 
       66.81        21.04         2.66        42.54        18.41        28.41 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       38.93        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                           0.13                            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 
                         13.365                          14.070 
[1] "0.1 - 115.7 (13.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D66V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10P11.21) MUTATED         1        1        3        3        23
  DEL PEAK 28(10P11.21) WILD-TYPE       9       20       44       30        64
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10P11.21) MUTATED          19         7         16          7
  DEL PEAK 28(10P11.21) WILD-TYPE        68        21         79         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         41       39         3
D66V3, multiclass
            clus
vv           DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  STAGE I                                1                               9
  STAGE IA                               1                              20
  STAGE IB                               3                              44
  STAGE II                               3                              30
  STAGE IIA                             23                              64
  STAGE IIB                             19                              68
  STAGE III                              7                              21
  STAGE IIIA                            16                              79
  STAGE IIIB                             7                              65
  STAGE IIIC                             5                              41
  STAGE IV                              10                              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 28(10P11.21) MUTATED       6  29  53   9
  DEL PEAK 28(10P11.21) WILD-TYPE    49 107 230 115
D66V4, multiclass
       clus
vv      DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  T0+T1                             6                              49
  T2                               29                             107
  T3                               53                             230
  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    34  30  18  14
  DEL PEAK 28(10P11.21) WILD-TYPE 173 157  80  82
D66V5, multiclass
    clus
vv   DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  N0                            34                             173
  N1                            30                             157
  N2                            18                              80
  N3                            14                              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"
D66V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    90   6
  DEL PEAK 28(10P11.21) WILD-TYPE 434  33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     90    6
  DEL PEAK 28(10P11.21) WILD-TYPE  434   33
   clus
vv  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  0                            90                             434
  1                             6                              33
[1] 2 2
[1] FALSE
D66V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    26  76
  DEL PEAK 28(10P11.21) WILD-TYPE 159 364
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     26   76
  DEL PEAK 28(10P11.21) WILD-TYPE  159  364
        clus
vv       DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  FEMALE                            26                             159
  MALE                              76                             364
[1] 2 2
[1] FALSE
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    68  26
  DEL PEAK 28(10P11.21) WILD-TYPE 377  93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     68   26
  DEL PEAK 28(10P11.21) WILD-TYPE  377   93
     clus
vv    DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  NO                             68                             377
  YES                            26                              93
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(10P11.21) MUTATED      32                         7
  DEL PEAK 28(10P11.21) WILD-TYPE   102                        10
                                 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      51
  DEL PEAK 28(10P11.21) WILD-TYPE   341
D66V11, multiclass
                                           clus
vv                                          DEL PEAK 28(10P11.21) MUTATED
  ASIAN                                                                32
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                51
                                           clus
vv                                          DEL PEAK 28(10P11.21) WILD-TYPE
  ASIAN                                                                 102
  BLACK OR AFRICAN AMERICAN                                              10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 341
[1] 4 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, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED     3  64
  DEL PEAK 28(10P11.21) WILD-TYPE   8 340
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED      3   64
  DEL PEAK 28(10P11.21) WILD-TYPE    8  340
                        clus
vv                       DEL PEAK 28(10P11.21) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       DEL PEAK 28(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             340
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 29(10Q22.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(10Q22.3) MUTATED    74  56
  DEL PEAK 29(10Q22.3) WILD-TYPE 280 189
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                           130                            469 
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                            56                            189 
$`DEL PEAK 29(10Q22.3) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4475 
        4.31        24.00         4.70        27.12         5.16        22.98 
TCGA-FP-A8CX TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
        0.23        25.78        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A50L 
        4.21        33.27        35.21         0.85         2.63         0.53 
TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OJ 
       23.41        14.50        23.18         3.16         0.30        21.01 
TCGA-L5-A4OQ TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NK TCGA-L5-A8NU 
        1.38         4.90         7.13        55.50        13.55        83.24 
TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       10.85        12.66        13.38        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        12.85        12.33        13.22        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR 
       12.00        12.23        12.03        13.38        13.18        12.26 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX 
       53.95         2.89         3.42        16.44        27.09        28.11 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-BR-4257 
       25.08        14.37         2.10         1.32        58.03         9.67 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 
       39.78        28.73         3.45        11.44        19.96        17.52 
TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-5799 
        5.39        20.22        13.87        34.98        21.44        13.02 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MG 
       13.35        12.53        12.33         6.31        12.43         6.58 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4466 
       12.20         7.99         4.01        14.01        12.03        18.97 
TCGA-CG-5718 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 
       36.00         4.01        19.13        18.54        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-EQ-8122 
       15.98        12.79        21.14        14.27        36.43         7.99 
TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 
       19.53         5.52         5.92        28.96        22.82        24.26 
TCGA-HU-A4GH TCGA-IN-8462 TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93H TCGA-R5-A7O7 
       11.77        18.81         6.74         6.51        37.64        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT 
        8.52         6.08         9.24         8.94         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
        5.46        13.02        18.48        22.19        17.85         1.87 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A92D TCGA-VQ-A94O 
       18.74         1.71         9.50         9.73        66.81        21.04 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-ZQ-A9CR 
       11.24        43.66        38.93         0.79 

$`DEL PEAK 29(10Q22.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI 
       15.68        60.39        34.85        18.28         8.94        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
       22.82         0.36        35.97        20.02        47.05        21.99 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       79.07        16.24        20.15         9.86        27.35        26.93 
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-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-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-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
      122.10        44.75        68.02         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43E 
       21.70        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        32.61        47.93        18.35         3.32         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.16        58.59        29.00         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       13.48        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-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U 
       10.45        12.43        13.41        12.33        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
       12.59        13.25        12.62        12.76        12.59        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO 
       11.54         4.47        10.52        13.18        12.33         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.03        12.85        33.11         7.82         8.02         7.59 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        5.06        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        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         8.98        25.81        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        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       41.23         3.42         2.66        19.73        26.70        11.70 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 
       19.56        11.01         9.47         9.44         6.61         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        4.64         7.43        18.35        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.34         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        36.16        35.24        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         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 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
        7.36        25.05         3.72        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       26.73        24.79        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        8.22        10.68        34.13         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18        11.21        12.10        12.76        12.59 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.07        12.82        12.43        12.30        11.31        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        1.02         8.05        54.08        29.98        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 
        9.01         7.07        12.00        30.97         6.97         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.66        20.91        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        17.19        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        14.66        20.91 
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        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-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-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 
       63.06        52.21        30.51        26.47         1.51        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.15        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
        3.39        18.38        12.46        13.35        19.53         6.44 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        36.95         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       18.21        74.53         4.60        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-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        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
        7.73        30.97        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-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        20.81        32.88        42.64        60.85 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
        5.72         2.66        42.54        18.41        28.41        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       17.13        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE 
                         13.02                          14.66 
[1] "0.2 - 83.2 (13.0)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(10Q22.3) MUTATED         2        4        7        6        23
  DEL PEAK 29(10Q22.3) WILD-TYPE       8       17       40       27        64
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(10Q22.3) MUTATED          21         9         22         12
  DEL PEAK 29(10Q22.3) WILD-TYPE        66        19         73         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 29(10Q22.3) MUTATED            8        9         2
  DEL PEAK 29(10Q22.3) WILD-TYPE         38       40         2
D67V3, multiclass
            clus
vv           DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  STAGE I                               2                              8
  STAGE IA                              4                             17
  STAGE IB                              7                             40
  STAGE II                              6                             27
  STAGE IIA                            23                             64
  STAGE IIB                            21                             66
  STAGE III                             9                             19
  STAGE IIIA                           22                             73
  STAGE IIIB                           12                             60
  STAGE IIIC                            8                             38
  STAGE IV                              9                             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 29(10Q22.3) MUTATED      10  37  64  15
  DEL PEAK 29(10Q22.3) WILD-TYPE    45  99 219 109
D67V4, multiclass
       clus
vv      DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  T0+T1                           10                             45
  T2                              37                             99
  T3                              64                            219
  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 29(10Q22.3) MUTATED    42  43  19  21
  DEL PEAK 29(10Q22.3) WILD-TYPE 165 144  79  75
D67V5, multiclass
    clus
vv   DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  N0                           42                            165
  N1                           43                            144
  N2                           19                             79
  N3                           21                             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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q22.3) MUTATED   114   9
  DEL PEAK 29(10Q22.3) WILD-TYPE 410  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q22.3) MUTATED    114    9
  DEL PEAK 29(10Q22.3) WILD-TYPE  410   30
   clus
vv  DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  0                          114                            410
  1                            9                             30
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q22.3) MUTATED    34 101
  DEL PEAK 29(10Q22.3) WILD-TYPE 151 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q22.3) MUTATED     34  101
  DEL PEAK 29(10Q22.3) WILD-TYPE  151  339
        clus
vv       DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  FEMALE                           34                            151
  MALE                            101                            339
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q22.3) MUTATED    95  27
  DEL PEAK 29(10Q22.3) WILD-TYPE 350  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q22.3) MUTATED     95   27
  DEL PEAK 29(10Q22.3) WILD-TYPE  350   92
     clus
vv    DEL PEAK 29(10Q22.3) MUTATED DEL PEAK 29(10Q22.3) WILD-TYPE
  NO                            95                            350
  YES                           27                             92
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(10Q22.3) MUTATED      36                         9
  DEL PEAK 29(10Q22.3) WILD-TYPE    98                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(10Q22.3) MUTATED                                           0
  DEL PEAK 29(10Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 29(10Q22.3) MUTATED      71
  DEL PEAK 29(10Q22.3) WILD-TYPE   321
D67V11, multiclass
                                           clus
vv                                          DEL PEAK 29(10Q22.3) MUTATED
  ASIAN                                                               36
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               71
                                           clus
vv                                          DEL PEAK 29(10Q22.3) WILD-TYPE
  ASIAN                                                                 98
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D67V12, binary
                                cls
clus                               0   1
  DEL PEAK 29(10Q22.3) MUTATED     4  84
  DEL PEAK 29(10Q22.3) WILD-TYPE   7 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(10Q22.3) MUTATED      4   84
  DEL PEAK 29(10Q22.3) WILD-TYPE    7  320
                        clus
vv                       DEL PEAK 29(10Q22.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 29(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            320
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 30(10Q23.31) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(10Q23.31) MUTATED    99  79
  DEL PEAK 30(10Q23.31) WILD-TYPE 255 166
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                            178                             421 
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                             79                             166 
$`DEL PEAK 30(10Q23.31) MUTATED`
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT TCGA-Q9-A6FU 
        4.31         8.94        24.00         4.70        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-2H-A9GF TCGA-2H-A9GI TCGA-2H-A9GL 
       47.05        21.99         0.23        25.78        14.30         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94        16.24         4.21        33.27        35.21         0.85 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6FA 
        2.63        18.64         0.53        23.41        14.50        44.75 
TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OO 
       23.18         3.16         0.30        32.61        21.01         3.32 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A8NE TCGA-L5-A8NI 
        3.16        58.59         4.90         7.13        55.50        13.48 
TCGA-L5-A8NK TCGA-L5-A8NU TCGA-L7-A56G TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O 
       13.55        83.24        10.85        10.45        12.66        13.41 
TCGA-LN-A49R TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.38        12.46        12.59        12.49        22.39        12.85 
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-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        13.38        13.18        12.26         7.59         5.06 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RC TCGA-V5-A7RE TCGA-VR-A8EP TCGA-VR-A8EX 
       53.95         2.89         3.42        16.44        27.09        28.11 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5818 
       25.08        14.37         2.10         1.32        58.03        11.70 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7716 
        6.61        18.35         9.67        13.87        35.24        39.78 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 
       28.73         3.45        37.25        11.44        19.96         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        34.98        21.44        13.02        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48A 
       12.76        12.59        12.53        12.33         6.31        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-4455 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       12.03        18.97        36.00        15.02         4.01        69.04 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       25.71        19.13        18.54        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 
       12.79        21.14        14.27        22.29         7.99         3.48 
TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 
       19.53        13.58         0.56         5.52         5.92        28.96 
TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD 
       22.82        11.77         6.51         6.58        23.80        33.40 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NU 
       18.81        18.38         6.44         6.74         6.51        11.70 
TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       37.64        36.95        45.67         8.52         6.08         9.24 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
        8.94         5.79         0.92        48.79         5.46        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A91A 
       18.48        22.19        17.85         1.87        13.35        39.45 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A928 
       18.74         1.71         9.50         9.73         9.04         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       38.93        26.04        16.14         0.79 

$`DEL PEAK 30(10Q23.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        34.85        18.28        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        0.36        35.97        20.02        22.98        79.07        16.24 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GJ 
       20.15         9.86        27.35        26.93        31.27        58.55 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YC 
        7.63         8.94        32.45         7.69        20.78        20.12 
TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A6QS 
        3.88         9.30        17.03         0.79        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        12.16       122.10        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       41.52        47.38        21.70        31.56        25.22        24.03 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        6.28        30.25        26.33        47.93        18.35         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        1.38        29.00         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ 
        7.40         3.75         3.02         2.66        12.92        16.47 
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-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N TCGA-LN-A49P 
       52.57        46.09        10.36         5.92        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.15        15.35        12.59        13.25        12.62        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ 
       12.59        15.52        11.54         4.47        12.23        13.18 
TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       12.33         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y2 
        8.02        16.31         7.04        38.40         6.35         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.30        12.69         7.00        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         8.98        25.81        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        33.70        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TI 
       41.23         3.42         2.66        19.73        26.70        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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        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        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        36.16        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       18.15        15.32         9.07        29.56        33.21        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       29.42         2.66        15.58         7.40         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 
       13.08         0.26        22.19         0.95        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        8.22        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        1.48        27.55        28.57        12.89         8.98         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65        20.42         1.15        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8527 
       13.41        13.15        13.18        11.21        12.10         7.17 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
       12.82        12.43        12.30        11.31        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02         3.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        8.05        54.08        19.07         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        12.03        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.66        20.91        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        13.35        17.19        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19        18.21        14.66 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       26.43        11.24        11.31        11.44        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27        11.38        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       59.54         5.03         6.21        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10        20.25         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       29.00        23.84        21.17        14.07        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39        12.46        13.35        19.53        12.59 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        15.75        13.51         2.53         5.56        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73        14.04        18.21        74.53         4.60 
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-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       16.87        19.04        13.25        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.50        12.79         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        20.81        32.88        42.64        60.85 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P 
       55.56         2.01        55.43         4.54         6.58         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        32.94        17.13        54.12        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                           0.23                            0.00 
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                          83.24                          122.30 
  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE 
                         13.285                          14.790 
[1] "0.2 - 83.2 (13.3)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.3"
D68V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(10Q23.31) MUTATED         4        5       14        9        27
  DEL PEAK 30(10Q23.31) WILD-TYPE       6       16       33       24        60
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(10Q23.31) MUTATED          26        10         29         18
  DEL PEAK 30(10Q23.31) WILD-TYPE        61        18         66         54
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 30(10Q23.31) MUTATED           11       13         2
  DEL PEAK 30(10Q23.31) WILD-TYPE         35       36         2
D68V3, multiclass
            clus
vv           DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  STAGE I                                4                               6
  STAGE IA                               5                              16
  STAGE IB                              14                              33
  STAGE II                               9                              24
  STAGE IIA                             27                              60
  STAGE IIB                             26                              61
  STAGE III                             10                              18
  STAGE IIIA                            29                              66
  STAGE IIIB                            18                              54
  STAGE IIIC                            11                              35
  STAGE IV                              13                              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
  DEL PEAK 30(10Q23.31) MUTATED      14  51  83  23
  DEL PEAK 30(10Q23.31) WILD-TYPE    41  85 200 101
D68V4, multiclass
       clus
vv      DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  T0+T1                            14                              41
  T2                               51                              85
  T3                               83                             200
  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 30(10Q23.31) MUTATED    59  56  26  30
  DEL PEAK 30(10Q23.31) WILD-TYPE 148 131  72  66
D68V5, multiclass
    clus
vv   DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  N0                            59                             148
  N1                            56                             131
  N2                            26                              72
  N3                            30                              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"
D68V6, binary
                                 cls
clus                                0   1
  DEL PEAK 30(10Q23.31) MUTATED   155  10
  DEL PEAK 30(10Q23.31) WILD-TYPE 369  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(10Q23.31) MUTATED    155   10
  DEL PEAK 30(10Q23.31) WILD-TYPE  369   29
   clus
vv  DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  0                           155                             369
  1                            10                              29
[1] 2 2
[1] FALSE
D68V7, binary
                                 cls
clus                                0   1
  DEL PEAK 30(10Q23.31) MUTATED    51 132
  DEL PEAK 30(10Q23.31) WILD-TYPE 134 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(10Q23.31) MUTATED     51  132
  DEL PEAK 30(10Q23.31) WILD-TYPE  134  308
        clus
vv       DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  FEMALE                            51                             134
  MALE                             132                             308
[1] 2 2
[1] FALSE
D68V8, binary
                                 cls
clus                                0   1
  DEL PEAK 30(10Q23.31) MUTATED   127  38
  DEL PEAK 30(10Q23.31) WILD-TYPE 318  81
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(10Q23.31) MUTATED    127   38
  DEL PEAK 30(10Q23.31) WILD-TYPE  318   81
     clus
vv    DEL PEAK 30(10Q23.31) MUTATED DEL PEAK 30(10Q23.31) WILD-TYPE
  NO                            127                             318
  YES                            38                              81
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(10Q23.31) MUTATED      44                        10
  DEL PEAK 30(10Q23.31) WILD-TYPE    90                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(10Q23.31) MUTATED                                           0
  DEL PEAK 30(10Q23.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 30(10Q23.31) MUTATED     103
  DEL PEAK 30(10Q23.31) WILD-TYPE   289
D68V11, multiclass
                                           clus
vv                                          DEL PEAK 30(10Q23.31) MUTATED
  ASIAN                                                                44
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               103
                                           clus
vv                                          DEL PEAK 30(10Q23.31) WILD-TYPE
  ASIAN                                                                  90
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 289
[1] 4 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, binary
                                 cls
clus                                0   1
  DEL PEAK 30(10Q23.31) MUTATED     4 111
  DEL PEAK 30(10Q23.31) WILD-TYPE   7 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(10Q23.31) MUTATED      4  111
  DEL PEAK 30(10Q23.31) WILD-TYPE    7  293
                        clus
vv                       DEL PEAK 30(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       DEL PEAK 30(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             293
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 31(11P15.5) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(11P15.5) MUTATED   105  67
  DEL PEAK 31(11P15.5) WILD-TYPE 249 178
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                           172                            427 
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                            67                            178 
$`DEL PEAK 31(11P15.5) MUTATED`
TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-S8-A6BV 
       34.85         4.31         8.94         4.70         0.36        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI 
       47.05        21.99        27.35        26.93        31.27        14.30 
TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
        5.92         4.21        32.45         7.69         0.85         2.63 
TCGA-IG-A50L TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OO 
        0.53        25.22         3.16         0.30        32.61         3.32 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 
        7.17         1.38         3.16        15.48         2.60         3.75 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
        3.02        55.50        13.48        16.47        13.55        13.22 
TCGA-L5-A8NS TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.41        10.85        10.36         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       12.62        12.59        12.49        12.76        12.85        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HY 
       13.22         4.47        12.33        25.25        12.00        12.03 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 
       13.18         0.13        12.85        38.40        53.95        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
        2.30        12.69         3.42        16.44         9.27         8.98 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-AA7B 
       27.09        12.43         8.12        28.11        18.18        11.24 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4184 
       15.91        25.08        14.37         2.10         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7703 TCGA-BR-7704 
       18.35         4.08         9.57        26.10        36.16        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 
       33.63        39.78        28.73         9.60         7.40        14.04 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        1.48         0.72         0.53        13.02        13.15        13.35 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-A48A TCGA-CG-4304 TCGA-CG-4443 
       12.76        12.59         7.17        12.43        27.02        29.98 
TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5717 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       19.07        18.97         6.97        12.03        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66        20.91        20.55        18.84        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A74A 
       10.26        15.22        15.98        21.14        14.27        19.96 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8211 TCGA-HF-7133 TCGA-HJ-7597 
        0.62        72.23        11.38        13.58        63.06        26.47 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-8462 
        5.92        18.15        22.75         2.10        23.80        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        13.35        19.53         6.44         6.74 
TCGA-IP-7968 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7C1 TCGA-RD-A8MW 
        2.53        37.64        45.67        18.21        16.67        37.91 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PK 
       18.48        37.41        37.22         7.73        22.19        17.85 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A925 
       13.35        14.33        21.83         9.73        55.56         4.54 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04        42.54        18.41        43.66 

$`DEL PEAK 31(11P15.5) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39        18.28        24.00        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97        27.12         5.16        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.23        20.15         9.86        25.78        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
       13.94         8.94        16.24        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 
       20.12        18.64         3.88         9.30        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H 
       23.41        12.82         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-A6FH TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
       47.38        21.70        23.18        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OS 
       30.25        26.33        21.01        47.93        18.35        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.13         7.43        25.12         7.40 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
        2.66        12.92         7.76         5.49        21.37         8.71 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y 
       83.24        52.57        46.09        12.59        13.25        12.46 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HX 
       12.59        22.39        15.52        11.54        10.52        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        12.33        13.38        12.03        12.26        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        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35         9.30         2.89         7.00        20.38         5.29 
TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EY 
       15.35        25.81        22.82         1.55        18.31        33.70 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T7 
       52.27        46.19        18.05         9.17        18.21        41.23 
TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 
        3.42         1.32         2.66        19.73        58.03        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 
       11.70        19.56        11.01         9.47         9.44         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 
        7.43        30.90         4.08         9.34         9.67         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.61        34.68        15.95        13.87        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-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       44.94        21.90         9.21        35.84        18.15        15.32 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44         0.69        29.59        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       29.42         2.66        19.96         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       26.33         4.31         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08        34.98        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        8.98        14.17        28.34         0.66        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 
        5.13        13.41        13.18        11.21        12.10        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.33        12.30        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.07        12.82        12.43         6.31        12.30        11.31 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.61         6.58        12.20        11.77        12.62        20.02 
TCGA-CG-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-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        0.99       105.07        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       25.71        19.13        18.61        17.85        13.35        17.19 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19        18.21        14.66        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.31        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
        4.34         7.13         7.99        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53        14.07        22.29        17.06        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        52.21        30.51 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        24.39        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        0.10         6.51         6.58        20.25         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       29.00        23.84        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       36.36         3.45        12.46        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       11.70        15.75        13.51         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        19.73        14.04         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61         5.13       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB 
       40.64       115.69       116.38        71.38        57.44        16.87 
TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       19.04         5.79         0.92        43.36        21.73        38.14 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH 
       30.97        34.29        46.26        16.31         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        73.41        39.45        11.70        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
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        66.81 
TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
        2.66        11.24        28.41        38.93        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE 
                         13.30                          14.66 
[1] "0.1 - 72.2 (13.3)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(11P15.5) MUTATED         4        5       11       12        24
  DEL PEAK 31(11P15.5) WILD-TYPE       6       16       36       21        63
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(11P15.5) MUTATED          18        14         30         13
  DEL PEAK 31(11P15.5) WILD-TYPE        69        14         65         59
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 31(11P15.5) MUTATED           12       11         2
  DEL PEAK 31(11P15.5) WILD-TYPE         34       38         2
D69V3, multiclass
            clus
vv           DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              5                             16
  STAGE IB                             11                             36
  STAGE II                             12                             21
  STAGE IIA                            24                             63
  STAGE IIB                            18                             69
  STAGE III                            14                             14
  STAGE IIIA                           30                             65
  STAGE IIIB                           13                             59
  STAGE IIIC                           12                             34
  STAGE IV                             11                             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
  DEL PEAK 31(11P15.5) MUTATED      16  44  82  21
  DEL PEAK 31(11P15.5) WILD-TYPE    39  92 201 103
D69V4, multiclass
       clus
vv      DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  T0+T1                           16                             39
  T2                              44                             92
  T3                              82                            201
  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 31(11P15.5) MUTATED    56  59  25  24
  DEL PEAK 31(11P15.5) WILD-TYPE 151 128  73  72
D69V5, multiclass
    clus
vv   DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  N0                           56                            151
  N1                           59                            128
  N2                           25                             73
  N3                           24                             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(11P15.5) MUTATED   141  11
  DEL PEAK 31(11P15.5) WILD-TYPE 383  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11P15.5) MUTATED    141   11
  DEL PEAK 31(11P15.5) WILD-TYPE  383   28
   clus
vv  DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  0                          141                            383
  1                           11                             28
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(11P15.5) MUTATED    38 137
  DEL PEAK 31(11P15.5) WILD-TYPE 147 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11P15.5) MUTATED     38  137
  DEL PEAK 31(11P15.5) WILD-TYPE  147  303
        clus
vv       DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  FEMALE                           38                            147
  MALE                            137                            303
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(11P15.5) MUTATED   113  43
  DEL PEAK 31(11P15.5) WILD-TYPE 332  76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11P15.5) MUTATED    113   43
  DEL PEAK 31(11P15.5) WILD-TYPE  332   76
     clus
vv    DEL PEAK 31(11P15.5) MUTATED DEL PEAK 31(11P15.5) WILD-TYPE
  NO                           113                            332
  YES                           43                             76
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(11P15.5) MUTATED      43                         8
  DEL PEAK 31(11P15.5) WILD-TYPE    91                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(11P15.5) MUTATED                                           0
  DEL PEAK 31(11P15.5) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 31(11P15.5) MUTATED     103
  DEL PEAK 31(11P15.5) WILD-TYPE   289
D69V11, multiclass
                                           clus
vv                                          DEL PEAK 31(11P15.5) MUTATED
  ASIAN                                                               43
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              103
                                           clus
vv                                          DEL PEAK 31(11P15.5) WILD-TYPE
  ASIAN                                                                 91
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                289
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 31(11P15.5) MUTATED     4 101
  DEL PEAK 31(11P15.5) WILD-TYPE   7 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11P15.5) MUTATED      4  101
  DEL PEAK 31(11P15.5) WILD-TYPE    7  303
                        clus
vv                       DEL PEAK 31(11P15.5) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       DEL PEAK 31(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            303
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 32(11Q25) MUTATION ANALYSIS
D70V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(11Q25) MUTATED   101  73
  DEL PEAK 32(11Q25) WILD-TYPE 253 172
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                         174                          425 
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                          73                          172 
$`DEL PEAK 32(11Q25) MUTATED`
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       27.12         5.16        20.02        14.30         7.63         5.92 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
       20.12        18.64         3.88        17.03        23.41         9.96 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FH TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF 
       14.50        12.16        47.38         3.16         0.30        26.33 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88S 
       47.93         3.32         7.17         3.16        29.00        15.48 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ 
        2.60         3.75         3.02        55.50        12.92        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.55        13.22        52.57        10.85        10.36         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49R TCGA-LN-A49V TCGA-LN-A49W 
       10.45        12.66        12.43        13.38        12.59        13.25 
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        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22        12.33        25.25        12.00        12.23 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18         0.13        12.03        12.85         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
        7.59         5.06         2.89         2.30        12.69         3.42 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ 
       25.81        12.43        18.31         8.12        28.11        18.18 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 
       11.24         9.17        15.91        25.08        41.23        14.37 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 
        2.10         1.32        58.03         6.97        18.35         6.18 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7715 
        9.57        17.29        13.68        26.10        12.16        33.63 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8365 
       37.25        11.44         9.60         2.66         7.40        17.52 
TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       20.22         8.22        34.98         1.48         0.72        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8527 
        1.15        21.44        13.02        13.15        12.10         7.17 
TCGA-CD-8532 TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5718 
       11.64        12.43         8.05        29.98        12.03        36.00 
TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       12.03        12.66        20.91        18.54        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       15.22        15.98        18.21        11.24        11.31        20.32 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 
       19.96         0.62        19.53        14.07        17.06        13.58 
TCGA-FP-8631 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 
        0.56        63.06        26.47         5.92        28.96         0.76 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
        3.25        22.75        11.77         6.58         2.10        23.84 
TCGA-HU-A4H6 TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IP-7968 TCGA-MX-A666 TCGA-R5-A7O7 
       21.17         6.44        10.62         2.53        14.04        45.67 
TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DT 
        9.24       122.30        37.91       115.69         8.94        48.79 
TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A 
       13.25         7.73         2.70        17.85        13.35        39.45 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       20.81        32.88         9.50        55.56         9.04        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6K 
       42.54        11.24        17.13        54.12        26.04        12.43 

$`DEL PEAK 32(11Q25) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M 
       15.68        60.39        34.85        18.28         4.31         8.94 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG 
       24.00         4.70        19.99        22.82         0.36        35.97 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR 
       58.55        13.94         8.94        16.24         4.21        32.45 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
        9.30         0.53         0.79        12.82        14.86         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
      122.10        44.75        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-A43E 
       23.18        31.56        25.22        24.03         6.28        30.25 
TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT 
       32.61        21.01        18.35         1.38        58.59         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NF TCGA-L5-A8NI 
        7.13         7.43        25.12         7.40         2.66        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-A8NW TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X 
       46.09        13.41        12.33        13.15        15.35        12.62 
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-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6L4 
       13.18        12.33        13.38        12.26        33.11        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.04        38.40         6.35        53.95         9.30        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00        20.38         5.29        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EY TCGA-VR-A8Q7 
        8.98        27.09        22.82         1.55        33.70        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       46.19        18.05        18.21         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-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 
        6.61         4.64         7.43        30.90         4.08         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.34         9.67         6.61        34.68        15.95        13.87 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        39.12         9.17        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       19.89         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       21.90         9.21        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       33.21        14.43         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
        0.56        29.42        19.96         2.20        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       31.10        13.08         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53        26.73        24.79        31.96        32.58         9.86 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88        10.68        34.13        13.87         7.53         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34         0.66        32.52         0.46        20.65        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.18        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.59        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4462 
        7.99        54.08         4.01        14.01        19.07         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       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-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       25.71        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       13.35        12.79        12.36        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       26.43        11.44        22.29        15.65         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         7.99        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM 
        3.48        22.29        59.54         5.03         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       77.29        52.21        30.51         1.51        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68        24.20        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       23.80        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38        12.46        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
        6.74        12.59         6.51        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56        63.62        37.64        36.95         3.72        19.73 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-RD-A7BS 
       18.21         8.52        74.53         6.08         4.60        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13        16.67        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       22.19         2.50        12.79         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        29.59        64.57        14.33        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       21.83        61.22        18.74         1.71        42.64        60.85 
TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A 
       66.81         2.66        18.41        43.66        28.41        38.93 
TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       32.94        16.14        27.55        17.26         0.79 

  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                        0.13                         0.00 
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                       122.3                        122.1 
  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE 
                       12.85                        15.35 
[1] "0.1 - 122.3 (12.8)" "0.0 - 122.1 (15.3)"
[1] "hr=" "1.2"
D70V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(11Q25) MUTATED         1        8        6       10        33
  DEL PEAK 32(11Q25) WILD-TYPE       9       13       41       23        54
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(11Q25) MUTATED          23        13         22         20
  DEL PEAK 32(11Q25) WILD-TYPE        64        15         73         52
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 32(11Q25) MUTATED           14       11         1
  DEL PEAK 32(11Q25) WILD-TYPE         32       38         3
D70V3, multiclass
            clus
vv           DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  STAGE I                             1                            9
  STAGE IA                            8                           13
  STAGE IB                            6                           41
  STAGE II                           10                           23
  STAGE IIA                          33                           54
  STAGE IIB                          23                           64
  STAGE III                          13                           15
  STAGE IIIA                         22                           73
  STAGE IIIB                         20                           52
  STAGE IIIC                         14                           32
  STAGE IV                           11                           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 32(11Q25) MUTATED      16  42  86  23
  DEL PEAK 32(11Q25) WILD-TYPE    39  94 197 101
D70V4, multiclass
       clus
vv      DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  T0+T1                         16                           39
  T2                            42                           94
  T3                            86                          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 32(11Q25) MUTATED    53  54  34  24
  DEL PEAK 32(11Q25) WILD-TYPE 154 133  64  72
D70V5, multiclass
    clus
vv   DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  N0                         53                          154
  N1                         54                          133
  N2                         34                           64
  N3                         24                           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"
D70V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(11Q25) MUTATED   143   9
  DEL PEAK 32(11Q25) WILD-TYPE 381  30
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(11Q25) MUTATED    143    9
  DEL PEAK 32(11Q25) WILD-TYPE  381   30
   clus
vv  DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  0                        143                          381
  1                          9                           30
[1] 2 2
[1] FALSE
D70V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(11Q25) MUTATED    40 138
  DEL PEAK 32(11Q25) WILD-TYPE 145 302
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(11Q25) MUTATED     40  138
  DEL PEAK 32(11Q25) WILD-TYPE  145  302
        clus
vv       DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  FEMALE                         40                          145
  MALE                          138                          302
[1] 2 2
[1] FALSE
D70V8, binary
                              cls
clus                             0   1
  DEL PEAK 32(11Q25) MUTATED   118  42
  DEL PEAK 32(11Q25) WILD-TYPE 327  77
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(11Q25) MUTATED    118   42
  DEL PEAK 32(11Q25) WILD-TYPE  327   77
     clus
vv    DEL PEAK 32(11Q25) MUTATED DEL PEAK 32(11Q25) WILD-TYPE
  NO                         118                          327
  YES                         42                           77
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(11Q25) MUTATED      44                         6
  DEL PEAK 32(11Q25) WILD-TYPE    90                        11
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 32(11Q25) MUTATED                                           0   110
  DEL PEAK 32(11Q25) WILD-TYPE                                         1   282
D70V11, multiclass
                                           clus
vv                                          DEL PEAK 32(11Q25) MUTATED
  ASIAN                                                             44
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                            110
                                           clus
vv                                          DEL PEAK 32(11Q25) WILD-TYPE
  ASIAN                                                               90
  BLACK OR AFRICAN AMERICAN                                           11
  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"
D70V12, binary
                              cls
clus                             0   1
  DEL PEAK 32(11Q25) MUTATED     6 114
  DEL PEAK 32(11Q25) WILD-TYPE   5 290
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(11Q25) MUTATED      6  114
  DEL PEAK 32(11Q25) WILD-TYPE    5  290
                        clus
vv                       DEL PEAK 32(11Q25) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        114
                        clus
vv                       DEL PEAK 32(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          290
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 33(12P13.1) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(12P13.1) MUTATED    59  51
  DEL PEAK 33(12P13.1) WILD-TYPE 295 194
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                           110                            489 
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                            51                            194 
$`DEL PEAK 33(12P13.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-S8-A6BV TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GR 
       34.85         8.94        20.02        25.78        13.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E 
       33.27         3.88         0.79        47.38        31.56        25.22 
TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       30.25        32.61         3.32         7.17         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH 
        4.90         7.13        15.48         3.75         3.02        12.92 
TCGA-L5-A8NN TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A7HW TCGA-LN-A7HY TCGA-M9-A5M8 
        5.49        52.57        12.66        12.00        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-X8-AAAR TCGA-Z6-A8JE TCGA-ZR-A9CJ 
        7.82         5.06        38.40        18.21         2.10        19.73 
TCGA-3M-AB46 TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 
       58.03         6.61         4.08         9.67         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 
       19.33        12.16        35.24        33.63         3.45        11.44 
TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 
        2.66        13.08        14.04         5.39        24.79         9.86 
TCGA-BR-A4CQ TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 
       34.98        13.15        12.76         7.17        12.82         6.31 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4441 
       11.31        12.43        12.20         3.02         7.99        14.01 
TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6817 
       30.97        15.02        69.04        20.55        15.22        12.79 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       12.33        14.27        19.96         0.62         7.99        72.23 
TCGA-HU-8245 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       18.15        23.84        23.80         3.39        18.38        13.35 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-RD-A8MW 
       11.70         2.53        36.95        14.04        45.67        37.91 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P3 TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       35.61         5.46        13.02        37.22         2.70         1.87 
TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Z 
       14.33        18.74         1.71        42.64         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-AA6D 
        9.04         2.01         5.72        66.81        21.04        17.13 
TCGA-VQ-AA6I TCGA-ZQ-A9CR 
       16.14         0.79 

$`DEL PEAK 33(12P13.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX 
       47.05        21.99        22.98        79.07        16.24         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI 
       20.15         9.86        27.35        26.93        31.27        14.30 
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-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC 
        7.69        35.21         0.85        20.78         2.63        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         9.30         0.53        17.03        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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C 
       44.75        68.02         3.68        41.52        21.70        23.18 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ 
       24.03         6.28         3.16         0.30        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88V 
       47.93        18.35         3.16        29.00         7.43         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
       25.12         7.40        55.50         2.66        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-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.59        13.25        12.62        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        12.85        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-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.23        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.03        12.85        12.26         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
        7.04         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        2.30        12.69         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 
       16.44        15.35         9.27         8.98        25.81        27.09 
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-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
        9.17        15.91        25.08        41.23        14.37         3.42 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        1.32         2.66        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         9.44         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       30.90         4.08         9.34         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-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       35.84        39.78        18.15        15.32        28.73         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        37.25        14.43         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        9.60        32.25         8.05         0.56        29.42        19.96 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.20        15.58         7.40         6.18        31.10         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-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        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       32.58        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        8.98         0.72        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       32.52        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       21.44        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.35        11.21        12.10        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
       20.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        29.98        19.07        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        12.00         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        25.71        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       20.91        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       13.35        17.19        10.26        15.98        12.36        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-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 
       22.29        15.65         8.38         4.34         7.13        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-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         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26         2.10        12.95        29.00        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ 
       15.68        33.40        36.36         3.45        18.81        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       19.53         6.44         6.74        12.59         6.51        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
       15.75        13.51         5.56        63.62        37.64         3.72 
TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       16.87        19.04         5.79         0.92        48.79        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        43.36        21.73        37.41        38.14         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       12.79        17.85         9.27        23.41        15.65        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 
       61.22        20.81        32.88        60.85         9.73        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        4.54         6.58         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       43.66        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                          0.62                           0.00 
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE 
                        13.115                         14.170 
[1] "0.6 - 72.2 (13.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(12P13.1) MUTATED         4        2       13        6        13
  DEL PEAK 33(12P13.1) WILD-TYPE       6       19       34       27        74
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(12P13.1) MUTATED          12         3         22         11
  DEL PEAK 33(12P13.1) WILD-TYPE        75        25         73         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 33(12P13.1) MUTATED            6       13         0
  DEL PEAK 33(12P13.1) WILD-TYPE         40       36         4
D71V3, multiclass
            clus
vv           DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              2                             19
  STAGE IB                             13                             34
  STAGE II                              6                             27
  STAGE IIA                            13                             74
  STAGE IIB                            12                             75
  STAGE III                             3                             25
  STAGE IIIA                           22                             73
  STAGE IIIB                           11                             61
  STAGE IIIC                            6                             40
  STAGE IV                             13                             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
  DEL PEAK 33(12P13.1) MUTATED       8  32  54  15
  DEL PEAK 33(12P13.1) WILD-TYPE    47 104 229 109
D71V4, multiclass
       clus
vv      DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  T0+T1                            8                             47
  T2                              32                            104
  T3                              54                            229
  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 33(12P13.1) MUTATED    36  35  18  19
  DEL PEAK 33(12P13.1) WILD-TYPE 171 152  80  77
D71V5, multiclass
    clus
vv   DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  N0                           36                            171
  N1                           35                            152
  N2                           18                             80
  N3                           19                             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"
D71V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(12P13.1) MUTATED    90   8
  DEL PEAK 33(12P13.1) WILD-TYPE 434  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(12P13.1) MUTATED     90    8
  DEL PEAK 33(12P13.1) WILD-TYPE  434   31
   clus
vv  DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  0                           90                            434
  1                            8                             31
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(12P13.1) MUTATED    34  79
  DEL PEAK 33(12P13.1) WILD-TYPE 151 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(12P13.1) MUTATED     34   79
  DEL PEAK 33(12P13.1) WILD-TYPE  151  361
        clus
vv       DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  FEMALE                           34                            151
  MALE                             79                            361
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(12P13.1) MUTATED    87  18
  DEL PEAK 33(12P13.1) WILD-TYPE 358 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(12P13.1) MUTATED     87   18
  DEL PEAK 33(12P13.1) WILD-TYPE  358  101
     clus
vv    DEL PEAK 33(12P13.1) MUTATED DEL PEAK 33(12P13.1) WILD-TYPE
  NO                            87                            358
  YES                           18                            101
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(12P13.1) MUTATED      17                         3
  DEL PEAK 33(12P13.1) WILD-TYPE   117                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(12P13.1) MUTATED                                           0
  DEL PEAK 33(12P13.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 33(12P13.1) MUTATED      74
  DEL PEAK 33(12P13.1) WILD-TYPE   318
D71V11, multiclass
                                           clus
vv                                          DEL PEAK 33(12P13.1) MUTATED
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               74
                                           clus
vv                                          DEL PEAK 33(12P13.1) WILD-TYPE
  ASIAN                                                                117
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  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"
D71V12, binary
                                cls
clus                               0   1
  DEL PEAK 33(12P13.1) MUTATED     2  61
  DEL PEAK 33(12P13.1) WILD-TYPE   9 343
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(12P13.1) MUTATED      2   61
  DEL PEAK 33(12P13.1) WILD-TYPE    9  343
                        clus
vv                       DEL PEAK 33(12P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 33(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            343
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 34(12Q23.1) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(12Q23.1) MUTATED    62  46
  DEL PEAK 34(12Q23.1) WILD-TYPE 292 199
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                           108                            491 
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                            46                            199 
$`DEL PEAK 34(12Q23.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A88Y TCGA-S8-A6BV TCGA-CG-4475 
       34.85        18.28         8.94         0.36        20.02        22.98 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GR 
       27.35        25.78        31.27        14.30        13.94        32.45 
TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H 
       33.27         2.63        18.64         0.79        23.41        14.50 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OJ 
       68.02        47.38        25.22        30.25        32.61        21.01 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A88V TCGA-L5-A893 
        3.32         7.17        58.59         7.13         2.60         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NS TCGA-L7-A56G 
       55.50         2.66        12.92        13.48        13.41        10.85 
TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A4A1 TCGA-LN-A5U6 TCGA-LN-A9FQ TCGA-Q9-A6FW 
       12.66        13.41        12.59        12.33        12.85         7.82 
TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASX TCGA-VR-A8ET 
        5.06         2.89        20.38         3.42         8.98         1.55 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-AAPN 
       52.27        11.24        18.21        25.08        14.37         2.66 
TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 
        6.61         9.67        17.29        35.24        33.63         3.45 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 
       11.44        29.42         7.40         5.39         9.21         9.86 
TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-8525 TCGA-CD-A489 TCGA-CD-A4MH 
        8.22        34.98        21.44        12.59        11.31        12.20 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 
       20.02         7.99        29.98        15.02        20.55        15.22 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8211 TCGA-HU-8249 TCGA-HU-A4GH TCGA-HU-A4H2 
        0.62         7.99        13.58        28.96        11.77        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RP TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 
       23.80        33.40         6.44        37.64        36.95        45.67 
TCGA-R5-A7ZE TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8PK TCGA-VQ-A8PS 
       18.21        35.61         5.46        18.48        17.85        13.35 
TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
       20.81        42.64        55.56         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        43.66        16.14        12.43         0.79 

$`DEL PEAK 34(12Q23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31        24.00         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4460 
       22.82        35.97        27.12         5.16        47.05        21.99 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U 
       79.07        16.24         0.23        20.15         9.86        26.93 
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-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS 
        7.69        35.21         0.85        20.78        20.12         3.88 
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-A6F8 TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        12.16       122.10        44.75         3.68        41.52 
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-A43H TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.30        26.33        47.93        18.35         1.38         3.16 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        4.90        29.00         7.43        15.48        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN 
        3.75        16.47        13.55        13.22         7.76         5.49 
TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       21.37         8.71        83.24        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.43        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 
       15.35        12.59        13.25        12.62        12.46        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        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.33        13.22         4.47        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.23        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ 
        0.13        12.03        12.26        33.11         8.02         7.59 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
       15.78         2.30        12.69         7.00         5.29        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       15.35         9.27        25.81        27.09        22.82        12.43 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D 
       18.31         8.12        28.11        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       18.05         9.17        15.91        41.23         3.42         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        1.32        19.73        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       11.01         9.47         9.44         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32        28.73         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       33.21        37.25        14.43         0.69        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       32.25         8.05         0.56         2.66        19.96         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       15.58         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       28.14         6.28         7.53        26.73        24.79        31.96 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       32.58        20.88        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        6.08         1.48        27.55        28.57        12.89         8.98 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.76        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.30        12.39        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
       12.82        12.43         6.31        12.30        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 
        1.02         8.05        54.08         4.01        14.01        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-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-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
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        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 
       11.44        20.32        22.29        15.65         8.38         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         7.13        14.47        72.23        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        3.48        19.53        14.07        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03         0.56         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.15        22.32        22.82        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        24.26        22.68        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.58        20.25         0.26         2.10        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       21.17        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38        12.46        13.35        19.53         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
        8.52        74.53         6.08         4.60         9.24        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         5.13        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-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-A8DZ 
       19.04         5.79         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       43.36        21.73        37.41        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W 
       21.83        61.22        18.74        32.88         1.71        60.85 
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-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        5.72        66.81         2.66        28.41        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-ZA-A8F6 
       17.13        54.12        26.04        27.55        17.26 

  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                          0.36                           0.00 
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                         68.02                         122.30 
  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE 
                        14.335                         13.870 
[1] "0.4 - 68.0 (14.3)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "1"  
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(12Q23.1) MUTATED         4        4        6        4        15
  DEL PEAK 34(12Q23.1) WILD-TYPE       6       17       41       29        72
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(12Q23.1) MUTATED          20         4         19          8
  DEL PEAK 34(12Q23.1) WILD-TYPE        67        24         76         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(12Q23.1) MUTATED            9        5         1
  DEL PEAK 34(12Q23.1) WILD-TYPE         37       44         3
D72V3, multiclass
            clus
vv           DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              4                             17
  STAGE IB                              6                             41
  STAGE II                              4                             29
  STAGE IIA                            15                             72
  STAGE IIB                            20                             67
  STAGE III                             4                             24
  STAGE IIIA                           19                             76
  STAGE IIIB                            8                             64
  STAGE IIIC                            9                             37
  STAGE IV                              5                             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 34(12Q23.1) MUTATED      16  18  58  12
  DEL PEAK 34(12Q23.1) WILD-TYPE    39 118 225 112
D72V4, multiclass
       clus
vv      DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  T0+T1                           16                             39
  T2                              18                            118
  T3                              58                            225
  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 34(12Q23.1) MUTATED    36  36  17  14
  DEL PEAK 34(12Q23.1) WILD-TYPE 171 151  81  82
D72V5, multiclass
    clus
vv   DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  N0                           36                            171
  N1                           36                            151
  N2                           17                             81
  N3                           14                             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"
D72V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(12Q23.1) MUTATED    89   5
  DEL PEAK 34(12Q23.1) WILD-TYPE 435  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12Q23.1) MUTATED     89    5
  DEL PEAK 34(12Q23.1) WILD-TYPE  435   34
   clus
vv  DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  0                           89                            435
  1                            5                             34
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(12Q23.1) MUTATED    32  78
  DEL PEAK 34(12Q23.1) WILD-TYPE 153 362
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12Q23.1) MUTATED     32   78
  DEL PEAK 34(12Q23.1) WILD-TYPE  153  362
        clus
vv       DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  FEMALE                           32                            153
  MALE                             78                            362
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(12Q23.1) MUTATED    74  27
  DEL PEAK 34(12Q23.1) WILD-TYPE 371  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12Q23.1) MUTATED     74   27
  DEL PEAK 34(12Q23.1) WILD-TYPE  371   92
     clus
vv    DEL PEAK 34(12Q23.1) MUTATED DEL PEAK 34(12Q23.1) WILD-TYPE
  NO                            74                            371
  YES                           27                             92
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(12Q23.1) MUTATED      19                         6
  DEL PEAK 34(12Q23.1) WILD-TYPE   115                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(12Q23.1) MUTATED                                           0
  DEL PEAK 34(12Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 34(12Q23.1) MUTATED      70
  DEL PEAK 34(12Q23.1) WILD-TYPE   322
D72V11, multiclass
                                           clus
vv                                          DEL PEAK 34(12Q23.1) MUTATED
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               70
                                           clus
vv                                          DEL PEAK 34(12Q23.1) WILD-TYPE
  ASIAN                                                                115
  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"
D72V12, binary
                                cls
clus                               0   1
  DEL PEAK 34(12Q23.1) MUTATED     3  55
  DEL PEAK 34(12Q23.1) WILD-TYPE   8 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(12Q23.1) MUTATED      3   55
  DEL PEAK 34(12Q23.1) WILD-TYPE    8  349
                        clus
vv                       DEL PEAK 34(12Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK 34(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            349
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 35(13Q12.11) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(13Q12.11) MUTATED    74  59
  DEL PEAK 35(13Q12.11) WILD-TYPE 280 186
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                            133                             466 
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                             59                             186 
$`DEL PEAK 35(13Q12.11) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43M TCGA-Q9-A6FU TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 
       60.39         8.94         5.16        47.05        22.98        79.07 
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        35.21 
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-A6FD TCGA-JY-A93C TCGA-JY-A93E 
       23.41         9.96         4.67        68.02        23.18        25.22 
TCGA-L5-A4OF TCGA-L5-A4OM TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A88S 
       26.33        47.93         3.16         4.90        29.00        15.48 
TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ 
       13.22         5.49        83.24        46.09        10.85        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        13.38 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.15        15.35        13.25        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX 
       22.39        12.85        11.54        12.33        10.52        12.23 
TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6KZ 
       12.03        12.33        13.38         0.13        12.26         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO 
       38.40         6.35         2.30        12.69        16.44        25.81 
TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       27.09        22.82        18.31        28.11        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       52.27        11.24        15.91        41.23        14.37         2.10 
TCGA-3M-AB46 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6564 
       58.03        19.56         6.97         4.08        17.29        26.10 
TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8297 
       12.16        33.63        39.78        33.21         2.66         7.40 
TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-8526 TCGA-CD-8527 
        9.86         1.48        12.89         0.66        12.53         7.17 
TCGA-CD-A486 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6525 
        6.31        18.97        12.03        15.02        20.91        13.35 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-FP-7916 
       10.26        12.36        18.21        16.44        15.65        14.07 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU 
       63.06         5.92         3.25        25.81        11.77         6.58 
TCGA-HU-A4H2 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR 
       12.95        18.81         3.39        12.46        13.35         6.74 
TCGA-IN-AB1X TCGA-KB-A93J TCGA-RD-A7BS TCGA-RD-A8N1 TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       13.51        36.95        11.05       115.69        13.25        13.02 
TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A92D 
        7.73         1.87        39.45        20.81         4.54        66.81 
TCGA-VQ-AA6G 
       26.04 

$`DEL PEAK 35(13Q12.11) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV 
       19.99        22.82         0.36        35.97        27.12        20.02 
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU 
       21.99        16.24         0.23        20.15         9.86        27.35 
TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       26.93        31.27        14.30         5.92        13.94        16.24 
TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT 
        4.21         7.69        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-A939 TCGA-JY-A93D 
       44.75         3.68        41.52        47.38        21.70        31.56 
TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH 
       24.03         6.28         3.16        30.25         0.30        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS 
       21.01        18.35         3.32         7.17         1.38        58.59 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.13         7.43         2.60        25.12         7.40         3.75 
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-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV 
       13.55         7.76        21.37         8.71        13.41        52.57 
TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A8 
       12.33        12.59        12.62        12.46        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ 
       12.33        13.22         4.47        25.25        12.00        13.18 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.59        16.31         7.04        53.95         9.30        15.78 
TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        2.89         7.00        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         8.98        12.43         1.55         8.12        46.19 
TCGA-VR-AA4G TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       18.05         9.17        18.21        25.08         3.42         1.32 
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-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-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-6707 TCGA-BR-6710 
        9.17        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       36.16        35.24        35.84        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       29.42        19.96         2.20        15.58         6.18        31.10 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
       13.08         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        6.28         7.53        26.73        24.79        31.96        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       20.88         8.22        10.68        34.13        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        6.08        34.98        27.55        28.57         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        28.34        32.52        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        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.41        13.02        13.15        13.18        13.35        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.10        12.76        12.59        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.59        11.64        15.39        12.07        12.82        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-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-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02         0.99       105.07        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       20.55        18.84        18.54        18.61        17.85        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        15.98        12.79        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-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       11.24        11.31        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        4.34        19.96         7.13         0.62         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        19.53        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       24.39        18.15        28.96        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-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 
       20.25         0.26         2.10        29.00        23.84        23.80 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       21.17        14.07        15.68        33.40        36.36         3.45 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       18.38        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        15.75         2.53         5.56        63.62        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.72        19.73        14.04        45.67        18.21         8.52 
TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24         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-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-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79         5.46        18.48        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX 
        9.27        23.41        15.65        13.35        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        73.41        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
       55.56         9.04         2.01        55.43         6.58         5.72 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I 
       28.41        38.93        32.94        17.13        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                           0.13                            0.00 
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                         115.69                          122.30 
  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE 
                          13.22                           14.38 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D73V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(13Q12.11) MUTATED         2        4       12        5        30
  DEL PEAK 35(13Q12.11) WILD-TYPE       8       17       35       28        57
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(13Q12.11) MUTATED          15        12         20         12
  DEL PEAK 35(13Q12.11) WILD-TYPE        72        16         75         60
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(13Q12.11) MUTATED            7        9         1
  DEL PEAK 35(13Q12.11) WILD-TYPE         39       40         3
D73V3, multiclass
            clus
vv           DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  STAGE I                                2                               8
  STAGE IA                               4                              17
  STAGE IB                              12                              35
  STAGE II                               5                              28
  STAGE IIA                             30                              57
  STAGE IIB                             15                              72
  STAGE III                             12                              16
  STAGE IIIA                            20                              75
  STAGE IIIB                            12                              60
  STAGE IIIC                             7                              39
  STAGE IV                               9                              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 35(13Q12.11) MUTATED      12  37  67  15
  DEL PEAK 35(13Q12.11) WILD-TYPE    43  99 216 109
D73V4, multiclass
       clus
vv      DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  T0+T1                            12                              43
  T2                               37                              99
  T3                               67                             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 35(13Q12.11) MUTATED    54  42  16  19
  DEL PEAK 35(13Q12.11) WILD-TYPE 153 145  82  77
D73V5, multiclass
    clus
vv   DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  N0                            54                             153
  N1                            42                             145
  N2                            16                              82
  N3                            19                              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"
D73V6, binary
                                 cls
clus                                0   1
  DEL PEAK 35(13Q12.11) MUTATED   115   7
  DEL PEAK 35(13Q12.11) WILD-TYPE 409  32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(13Q12.11) MUTATED    115    7
  DEL PEAK 35(13Q12.11) WILD-TYPE  409   32
   clus
vv  DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  0                           115                             409
  1                             7                              32
[1] 2 2
[1] FALSE
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(13Q12.11) MUTATED    22 116
  DEL PEAK 35(13Q12.11) WILD-TYPE 163 324
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(13Q12.11) MUTATED     22  116
  DEL PEAK 35(13Q12.11) WILD-TYPE  163  324
        clus
vv       DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  FEMALE                            22                             163
  MALE                             116                             324
[1] 2 2
[1] FALSE
D73V8, binary
                                 cls
clus                                0   1
  DEL PEAK 35(13Q12.11) MUTATED    96  35
  DEL PEAK 35(13Q12.11) WILD-TYPE 349  84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(13Q12.11) MUTATED     96   35
  DEL PEAK 35(13Q12.11) WILD-TYPE  349   84
     clus
vv    DEL PEAK 35(13Q12.11) MUTATED DEL PEAK 35(13Q12.11) WILD-TYPE
  NO                             96                             349
  YES                            35                              84
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(13Q12.11) MUTATED      38                         3
  DEL PEAK 35(13Q12.11) WILD-TYPE    96                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(13Q12.11) MUTATED                                           0
  DEL PEAK 35(13Q12.11) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 35(13Q12.11) MUTATED      81
  DEL PEAK 35(13Q12.11) WILD-TYPE   311
D73V11, multiclass
                                           clus
vv                                          DEL PEAK 35(13Q12.11) MUTATED
  ASIAN                                                                38
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                81
                                           clus
vv                                          DEL PEAK 35(13Q12.11) WILD-TYPE
  ASIAN                                                                  96
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 311
[1] 4 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, binary
                                 cls
clus                                0   1
  DEL PEAK 35(13Q12.11) MUTATED     4  85
  DEL PEAK 35(13Q12.11) WILD-TYPE   7 319
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(13Q12.11) MUTATED      4   85
  DEL PEAK 35(13Q12.11) WILD-TYPE    7  319
                        clus
vv                       DEL PEAK 35(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            85
                        clus
vv                       DEL PEAK 35(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             319
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 36(13Q21.31) MUTATION ANALYSIS
D74V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(13Q21.31) MUTATED    72  51
  DEL PEAK 36(13Q21.31) WILD-TYPE 282 194
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                            123                             476 
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                             51                             194 
$`DEL PEAK 36(13Q21.31) MUTATED`
TCGA-JY-A6FB TCGA-L5-A4OE TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-2H-A9GJ 
       60.39        24.00        47.05        22.98        79.07        58.55 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        7.63         8.94        32.45        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A6QS 
        2.63         3.88         0.53        17.03        23.41         9.96 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
       44.75        68.02        25.22        26.33        21.01        47.93 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NN 
        3.16        29.00         2.60        13.48        13.22         5.49 
TCGA-L5-A8NU TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       83.24        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41        13.38        13.15        15.35        13.25 
TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4MR 
       12.46        12.49        12.76        22.39        12.85        13.22 
TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.33        10.52        12.23        12.03        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XQ 
       13.18         0.13        12.26         7.59         5.06         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-V5-A7RE TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ 
        9.30        12.69        16.44        25.81        27.09        22.82 
TCGA-VR-A8EU TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-XP-A8T8 
       18.31        28.11        18.18        52.27        15.91        14.37 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7716 
        6.61         6.97         4.08        26.10        12.16        39.78 
TCGA-BR-8297 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 
        7.40        20.22         9.86         1.48        12.89         0.66 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A487 
       12.53         7.17        12.33        12.39         6.31        12.30 
TCGA-CG-4301 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5733 TCGA-D7-6520 
        3.02        18.97        30.97        36.00        21.07        18.84 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       13.35        17.19        12.79        18.21        14.66        21.14 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A74A TCGA-FP-7916 TCGA-FP-8211 TCGA-HF-7133 
       16.44        13.78        19.96        14.07        13.58        63.06 
TCGA-HU-A4GC TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RR 
        3.25        12.95         3.45        18.81        12.46         6.74 
TCGA-KB-A93J TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91A TCGA-VQ-A925 
       36.95        11.05         7.73         1.87        39.45         4.54 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I 
       38.93        54.12        16.14 

$`DEL PEAK 36(13Q21.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        34.85        18.28         4.31         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       20.02        21.99        16.24         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL 
       27.35        26.93        25.78        31.27        14.30         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YC 
       13.94        16.24         4.21         7.69        33.27        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A7DP TCGA-IG-A8O2 
       18.64         9.30         0.79        12.82        14.86         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       14.50        12.16       122.10         3.68        41.52        47.38 
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-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25         0.30        32.61        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S 
        1.38        58.59         4.90         7.13         7.43        15.48 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF 
       25.12         7.40         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR 
       12.92        16.47        13.55         7.76        21.37         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X 
       13.41        52.57        12.66        12.33        12.59        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 
       12.59        12.59        15.52        11.54        12.33         4.47 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 
       25.25        12.00        13.18        12.03        12.85        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 
        7.82         8.02        16.31         7.04        38.40        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB 
       15.78         2.89         2.30         7.00        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35         9.27         8.98        12.43         1.55 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
        8.12        33.70        46.19        18.05        11.24         9.17 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        41.23         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        2.66        19.73        58.03        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       11.01         9.47         9.44         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         9.34         9.67         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-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        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       33.21        37.25        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       19.96         2.20        15.58         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       14.04         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 
       25.05         3.72         5.39        25.18         9.21         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 
       26.73        24.79        31.96        32.58        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.34        32.52        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        21.44        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.59        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.82        12.43        11.31        12.43        11.61         6.58 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-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-4469 
       29.98        19.07        12.03         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        25.71        12.66        20.91        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        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        17.19        20.91        14.27         5.92        36.43 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        26.43        11.24        11.31        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-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-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        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         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI 
       14.07        15.68        33.40        36.36         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       13.35        19.53         6.44        12.59         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       11.70        15.75        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       37.64         3.72        19.73        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT 
        8.52        74.53         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        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22        30.97        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-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        13.35        29.59        64.57        14.33        73.41 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.71        42.64        60.85         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.04         2.01        55.43         6.58         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       21.04         2.66        42.54        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       28.41        32.94        17.13        26.04        27.55        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                           0.13                            0.00 
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                          83.24                          122.30 
  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE 
                         13.250                          14.315 
[1] "0.1 - 83.2 (13.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D74V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(13Q21.31) MUTATED         3        5        6        6        24
  DEL PEAK 36(13Q21.31) WILD-TYPE       7       16       41       27        63
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(13Q21.31) MUTATED          16        12         23         12
  DEL PEAK 36(13Q21.31) WILD-TYPE        71        16         72         60
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 36(13Q21.31) MUTATED            6        4         1
  DEL PEAK 36(13Q21.31) WILD-TYPE         40       45         3
D74V3, multiclass
            clus
vv           DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  STAGE I                                3                               7
  STAGE IA                               5                              16
  STAGE IB                               6                              41
  STAGE II                               6                              27
  STAGE IIA                             24                              63
  STAGE IIB                             16                              71
  STAGE III                             12                              16
  STAGE IIIA                            23                              72
  STAGE IIIB                            12                              60
  STAGE IIIC                             6                              40
  STAGE IV                               4                              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 36(13Q21.31) MUTATED      14  33  60  13
  DEL PEAK 36(13Q21.31) WILD-TYPE    41 103 223 111
D74V4, multiclass
       clus
vv      DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  T0+T1                            14                              41
  T2                               33                             103
  T3                               60                             223
  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 36(13Q21.31) MUTATED    46  42  14  17
  DEL PEAK 36(13Q21.31) WILD-TYPE 161 145  84  79
D74V5, multiclass
    clus
vv   DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  N0                            46                             161
  N1                            42                             145
  N2                            14                              84
  N3                            17                              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"
D74V6, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q21.31) MUTATED   106   4
  DEL PEAK 36(13Q21.31) WILD-TYPE 418  35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q21.31) MUTATED    106    4
  DEL PEAK 36(13Q21.31) WILD-TYPE  418   35
   clus
vv  DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  0                           106                             418
  1                             4                              35
[1] 2 2
[1] FALSE
D74V7, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q21.31) MUTATED    27  99
  DEL PEAK 36(13Q21.31) WILD-TYPE 158 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q21.31) MUTATED     27   99
  DEL PEAK 36(13Q21.31) WILD-TYPE  158  341
        clus
vv       DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  FEMALE                            27                             158
  MALE                              99                             341
[1] 2 2
[1] FALSE
D74V8, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q21.31) MUTATED    82  38
  DEL PEAK 36(13Q21.31) WILD-TYPE 363  81
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q21.31) MUTATED     82   38
  DEL PEAK 36(13Q21.31) WILD-TYPE  363   81
     clus
vv    DEL PEAK 36(13Q21.31) MUTATED DEL PEAK 36(13Q21.31) WILD-TYPE
  NO                             82                             363
  YES                            38                              81
[1] 2 2
[1] FALSE
D74V9, continuous
D74V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(13Q21.31) MUTATED      38                         2
  DEL PEAK 36(13Q21.31) WILD-TYPE    96                        15
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(13Q21.31) MUTATED                                           0
  DEL PEAK 36(13Q21.31) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 36(13Q21.31) MUTATED      71
  DEL PEAK 36(13Q21.31) WILD-TYPE   321
D74V11, multiclass
                                           clus
vv                                          DEL PEAK 36(13Q21.31) MUTATED
  ASIAN                                                                38
  BLACK OR AFRICAN AMERICAN                                             2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                71
                                           clus
vv                                          DEL PEAK 36(13Q21.31) WILD-TYPE
  ASIAN                                                                  96
  BLACK OR AFRICAN AMERICAN                                              15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  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"
D74V12, binary
                                 cls
clus                                0   1
  DEL PEAK 36(13Q21.31) MUTATED     3  76
  DEL PEAK 36(13Q21.31) WILD-TYPE   8 328
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(13Q21.31) MUTATED      3   76
  DEL PEAK 36(13Q21.31) WILD-TYPE    8  328
                        clus
vv                       DEL PEAK 36(13Q21.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            76
                        clus
vv                       DEL PEAK 36(13Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             328
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 37(14Q23.3) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(14Q23.3) MUTATED    99  83
  DEL PEAK 37(14Q23.3) WILD-TYPE 255 162
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                           182                            417 
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                            83                            162 
$`DEL PEAK 37(14Q23.3) MUTATED`
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        18.28         8.94        24.00         4.70         0.36 
TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GN 
       16.24        27.35        26.93        31.27         7.63         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A8O2 
       16.24         4.21        35.21        23.41        12.82         4.67 
TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OF 
       14.50       122.10        47.38        25.22         0.30        26.33 
TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A891 TCGA-L5-A8NE 
        3.16        29.00         7.13        15.48         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49W 
        2.66        16.47        10.85        10.36        10.45        13.25 
TCGA-LN-A4A1 TCGA-LN-A7HV TCGA-LN-A7HY TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.59        10.52        12.03        33.11         7.59         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ 
        6.35         9.30        15.78         7.00        25.81        22.82 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       12.43        18.31        52.27        18.05         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 
       58.03        19.56        11.01         9.44         6.61         4.08 
TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        9.67         9.57        17.29        19.33        26.10         9.17 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        33.63        39.78        28.73        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8373 
       37.25        11.44        29.42         2.66        31.10        14.79 
TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8678 
        7.36         5.39        25.18         9.21        27.12        24.79 
TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
       20.88         7.53        34.98         1.48         0.72         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 TCGA-CD-5803 
       32.52         0.46        20.65         1.15        13.18        11.21 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 
       12.76         7.17        15.39        12.07        12.82        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 
       14.01        18.97        30.97        15.02        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8576 
       18.54        13.35        17.19        10.26        15.98        14.66 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-A72C 
       16.44        11.31        11.44        22.29         7.99        11.38 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 
       14.07        17.06         0.56        26.47        18.15        28.96 
TCGA-HU-A4G3 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H5 
        5.59         3.25        11.77         8.98         2.10        23.80 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       33.40        36.36        13.35        19.53         6.44         6.74 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 TCGA-RD-A7C1 
       11.70         2.53         5.56        37.64        14.04        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU 
      122.30        37.91       115.69         8.94         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        18.48        43.36        37.22         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PX 
       46.26        12.79         2.70        17.85        13.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 
       14.33        73.41        18.74        20.81        55.56         9.04 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       66.81        21.04        42.54        18.41        38.93        32.94 
TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       26.04         0.79 

$`DEL PEAK 37(14Q23.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        34.85         4.31        19.99        22.82        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 
       27.12         5.16        20.02        47.05        21.99        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF TCGA-2H-A9GI 
       79.07         0.23        20.15         9.86        25.78        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 
       58.55         5.92        13.94        32.45         7.69        33.27 
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-A6QS TCGA-IG-A7DP 
        9.30         0.53        17.03         0.79         9.96        14.86 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16        44.75        68.02         3.68        41.52        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-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       32.61        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88W 
        1.38        58.59         4.90         7.43         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
        7.40         3.02        12.92        13.48        13.55        13.22 
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-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       52.57        46.09         5.92        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        12.59        12.62 
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        12.85 
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-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       25.25        12.00        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        12.26         7.82 
TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 
        8.02        16.31         7.04        38.40        53.95         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69        20.38         5.29         3.42        16.44 
TCGA-V5-AASV TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ET TCGA-VR-A8EW 
       15.35         9.27         8.98        27.09         1.55         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        18.18        46.19        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD 
       15.91        18.21        25.08        41.23        14.37         3.42 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 
        2.10         1.32        26.70        11.70         9.47         6.97 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 
        4.64         7.43        18.35        30.90         4.08         9.34 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        6.18         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        40.21        30.90        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       36.16        35.84        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       29.56        14.43         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        8.05         0.56        19.96         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        31.27 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 
       25.05         3.72        20.22         1.12        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
        9.86         8.22        10.68        34.13        13.87         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       28.34        13.51        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8525 
       13.41        13.02        13.15        13.35        12.10        12.59 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.53        12.33        12.30        12.39        12.59        11.64 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43         6.31        12.30        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       29.98        19.07        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-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-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       19.13        18.61        17.85        15.22        12.79        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       18.21        21.14        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.78        14.76        26.43        11.24        20.32        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         0.62        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 
       72.23        21.27         3.48        19.53        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        5.03        13.58         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51         1.51         5.92        24.39        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.20        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 
       23.84        21.17        14.07        15.68         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
        3.39        18.38        12.46        12.59         6.51        10.62 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ 
       15.75        13.51        63.62        36.95         3.72        19.73 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 
        9.24        11.05         8.61         5.13        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-A8P8 TCGA-VQ-A8PB 
       48.79        21.73        37.41        38.14        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31        22.19         2.50         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       15.65        29.59        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
        2.01        55.43         4.54         6.58         5.72         2.66 
TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I 
       11.24        43.66        28.41        17.13        54.12        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                           0.3                            0.0 
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE 
                        14.725                         13.550 
[1] "0.3 - 122.3 (14.7)" "0.0 - 116.4 (13.6)"
[1] "hr=" "1.1"
D75V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(14Q23.3) MUTATED         3        3       14       11        25
  DEL PEAK 37(14Q23.3) WILD-TYPE       7       18       33       22        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(14Q23.3) MUTATED          23         9         35         25
  DEL PEAK 37(14Q23.3) WILD-TYPE        64        19         60         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 37(14Q23.3) MUTATED           12        9         3
  DEL PEAK 37(14Q23.3) WILD-TYPE         34       40         1
D75V3, multiclass
            clus
vv           DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  STAGE I                               3                              7
  STAGE IA                              3                             18
  STAGE IB                             14                             33
  STAGE II                             11                             22
  STAGE IIA                            25                             62
  STAGE IIB                            23                             64
  STAGE III                             9                             19
  STAGE IIIA                           35                             60
  STAGE IIIB                           25                             47
  STAGE IIIC                           12                             34
  STAGE IV                              9                             40
  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 37(14Q23.3) MUTATED      14  36  91  37
  DEL PEAK 37(14Q23.3) WILD-TYPE    41 100 192  87
D75V4, multiclass
       clus
vv      DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  T0+T1                           14                             41
  T2                              36                            100
  T3                              91                            192
  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 37(14Q23.3) MUTATED    54  57  40  23
  DEL PEAK 37(14Q23.3) WILD-TYPE 153 130  58  73
D75V5, multiclass
    clus
vv   DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  N0                           54                            153
  N1                           57                            130
  N2                           40                             58
  N3                           23                             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"
D75V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(14Q23.3) MUTATED   154   8
  DEL PEAK 37(14Q23.3) WILD-TYPE 370  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(14Q23.3) MUTATED    154    8
  DEL PEAK 37(14Q23.3) WILD-TYPE  370   31
   clus
vv  DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  0                          154                            370
  1                            8                             31
[1] 2 2
[1] FALSE
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(14Q23.3) MUTATED    51 136
  DEL PEAK 37(14Q23.3) WILD-TYPE 134 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(14Q23.3) MUTATED     51  136
  DEL PEAK 37(14Q23.3) WILD-TYPE  134  304
        clus
vv       DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  FEMALE                           51                            134
  MALE                            136                            304
[1] 2 2
[1] FALSE
D75V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(14Q23.3) MUTATED   134  36
  DEL PEAK 37(14Q23.3) WILD-TYPE 311  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(14Q23.3) MUTATED    134   36
  DEL PEAK 37(14Q23.3) WILD-TYPE  311   83
     clus
vv    DEL PEAK 37(14Q23.3) MUTATED DEL PEAK 37(14Q23.3) WILD-TYPE
  NO                           134                            311
  YES                           36                             83
[1] 2 2
[1] FALSE
D75V9, continuous
D75V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(14Q23.3) MUTATED      34                         4
  DEL PEAK 37(14Q23.3) WILD-TYPE   100                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(14Q23.3) MUTATED                                           0
  DEL PEAK 37(14Q23.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 37(14Q23.3) MUTATED     124
  DEL PEAK 37(14Q23.3) WILD-TYPE   268
D75V11, multiclass
                                           clus
vv                                          DEL PEAK 37(14Q23.3) MUTATED
  ASIAN                                                               34
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              124
                                           clus
vv                                          DEL PEAK 37(14Q23.3) WILD-TYPE
  ASIAN                                                                100
  BLACK OR AFRICAN AMERICAN                                             13
  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"
D75V12, binary
                                cls
clus                               0   1
  DEL PEAK 37(14Q23.3) MUTATED     2 112
  DEL PEAK 37(14Q23.3) WILD-TYPE   9 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(14Q23.3) MUTATED      2  112
  DEL PEAK 37(14Q23.3) WILD-TYPE    9  292
                        clus
vv                       DEL PEAK 37(14Q23.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 37(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 38(15Q11.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(15Q11.2) MUTATED   107  68
  DEL PEAK 38(15Q11.2) WILD-TYPE 247 177
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                           175                            424 
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                            68                            177 
$`DEL PEAK 38(15Q11.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NT 
       34.85        18.28         8.94        24.00         4.70        27.12 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
        5.16        20.02        47.05         0.23         9.86        26.93 
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        35.21 
TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A625 TCGA-IG-A97H TCGA-JY-A93C TCGA-JY-A93D 
       20.12         3.88        12.82        14.50        23.18        31.56 
TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OT TCGA-L5-A4OU 
       25.22         0.30        32.61        47.93         4.90        29.00 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NN TCGA-L5-A8NR 
        3.02        55.50         2.66        12.92         5.49         8.71 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49R TCGA-LN-A4A1 TCGA-LN-A4A5 
       13.41        83.24        10.45        13.38        12.59        22.39 
TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HY TCGA-LN-A8I0 
       15.52        12.33        12.33        25.25        12.03        13.38 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 
        0.13        12.85        12.26         7.59         5.06        16.31 
TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE 
       38.40         9.30         7.00        20.38         3.42        16.44 
TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-X8-AAAR TCGA-XP-A8T8 TCGA-Z6-A8JD 
       25.81        28.11        18.18        18.21        14.37         3.42 
TCGA-Z6-A8JE TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 
        2.10        11.01         9.67        13.68        19.33         9.17 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 
       36.16        35.24         3.45        29.42         2.66        14.79 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4J1 
        5.39         9.21        20.88        10.68        34.98         0.72 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
       20.65        21.44        13.18        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A48C 
        7.17        12.30        12.39        12.82        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 
       12.20        20.02         7.99        54.08         4.01        18.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6518 
        1.02        12.03        15.02        69.04        12.66        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       20.55        18.84        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 
       15.98        12.79        18.21        14.66        11.31        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8211 TCGA-FP-A4BF 
       15.65        19.96         7.99        72.23        13.58         5.52 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GC 
       63.06        26.47        18.15        28.96        22.82         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
       25.81        11.77         8.98         6.58         2.10        23.84 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A7NT 
       21.17        33.40        18.38        12.46        13.35        10.62 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-R5-A7ZF TCGA-R5-A805 
       11.70         2.53        63.62        36.95         8.52         9.24 
TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
       11.05        16.67        37.91       115.69        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS 
        0.92        48.79         5.46        37.41        17.85        13.35 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       73.41        18.74        20.81         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       55.56        66.81        42.54        43.66        32.94        54.12 
TCGA-VQ-AA6I 
       16.14 

$`DEL PEAK 38(15Q11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-L5-A8NG TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       35.97        21.99        22.98        79.07        16.24        20.15 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GM 
       27.35        25.78        31.27        14.30        58.55        13.94 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        8.94         4.21        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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93F 
       68.02         3.68        41.52        47.38        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
        6.28         3.16        30.25        26.33        21.01        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OW 
        3.32         7.17         1.38         3.16        58.59         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
        7.43        15.48         2.60        25.12         7.40         3.75 
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-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49M 
       52.57        46.09        10.85        10.36         5.92        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        13.41        12.33        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        12.46        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.85        11.54        13.22         4.47        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-M9-A5M8 
       12.23        13.18        12.33        13.18        12.03        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 
        7.82         8.02         7.04         6.35        53.95        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASW 
        2.89         2.30        12.69         5.29        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        33.70        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        15.91        25.08        41.23         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       19.73        58.03        26.70        11.70        19.56         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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
       30.90         4.08         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-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        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        35.84        33.63        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       28.73         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.56        19.96         2.20        15.58         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       31.10        13.08         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       26.33         4.31        14.04         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72        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        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 
       26.73        24.79        31.96        32.58         9.86         8.22 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52        13.51         0.46        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       16.14         5.13        13.41        13.02        13.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       11.21        12.76        12.33        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
       12.07        12.43         6.31        12.30        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        8.05        14.01        29.98        19.07        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        9.01         7.07        12.00        30.97         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6521 
        4.01        21.07         7.99        25.71        20.91        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       18.61        17.85        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44        20.32         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        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-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        52.21        30.51         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        22.32        21.07         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        22.68        24.20        22.75        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26        12.95        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.80        14.07        15.68        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
        3.39        19.53         6.44         6.74        12.59         6.51 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
       15.75        13.51         5.56        37.64         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       14.04        45.67        18.21        74.53         6.08         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-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        16.87        19.04        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       18.48        43.36        21.73        38.14        37.22         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
       30.97        34.29        46.26        16.31        22.19         2.50 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       29.59        64.57        14.33        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A922 TCGA-VQ-A923 
       61.22        32.88        42.64        60.85         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58         5.72        21.04         2.66 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G 
       11.24        18.41        28.41        38.93        17.13        26.04 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE 
                        13.680                         13.975 
[1] "0.1 - 115.7 (13.7)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(15Q11.2) MUTATED         4        6       13        8        25
  DEL PEAK 38(15Q11.2) WILD-TYPE       6       15       34       25        62
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(15Q11.2) MUTATED          24         8         35         20
  DEL PEAK 38(15Q11.2) WILD-TYPE        63        20         60         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 38(15Q11.2) MUTATED            8       14         3
  DEL PEAK 38(15Q11.2) WILD-TYPE         38       35         1
D76V3, multiclass
            clus
vv           DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              6                             15
  STAGE IB                             13                             34
  STAGE II                              8                             25
  STAGE IIA                            25                             62
  STAGE IIB                            24                             63
  STAGE III                             8                             20
  STAGE IIIA                           35                             60
  STAGE IIIB                           20                             52
  STAGE IIIC                            8                             38
  STAGE IV                             14                             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 38(15Q11.2) MUTATED      18  41  93  22
  DEL PEAK 38(15Q11.2) WILD-TYPE    37  95 190 102
D76V4, multiclass
       clus
vv      DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  T0+T1                           18                             37
  T2                              41                             95
  T3                              93                            190
  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 38(15Q11.2) MUTATED    60  55  33  23
  DEL PEAK 38(15Q11.2) WILD-TYPE 147 132  65  73
D76V5, multiclass
    clus
vv   DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  N0                           60                            147
  N1                           55                            132
  N2                           33                             65
  N3                           23                             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"
D76V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(15Q11.2) MUTATED   152  12
  DEL PEAK 38(15Q11.2) WILD-TYPE 372  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(15Q11.2) MUTATED    152   12
  DEL PEAK 38(15Q11.2) WILD-TYPE  372   27
   clus
vv  DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  0                          152                            372
  1                           12                             27
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(15Q11.2) MUTATED    50 133
  DEL PEAK 38(15Q11.2) WILD-TYPE 135 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(15Q11.2) MUTATED     50  133
  DEL PEAK 38(15Q11.2) WILD-TYPE  135  307
        clus
vv       DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  FEMALE                           50                            135
  MALE                            133                            307
[1] 2 2
[1] FALSE
D76V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(15Q11.2) MUTATED   125  41
  DEL PEAK 38(15Q11.2) WILD-TYPE 320  78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(15Q11.2) MUTATED    125   41
  DEL PEAK 38(15Q11.2) WILD-TYPE  320   78
     clus
vv    DEL PEAK 38(15Q11.2) MUTATED DEL PEAK 38(15Q11.2) WILD-TYPE
  NO                           125                            320
  YES                           41                             78
[1] 2 2
[1] FALSE
D76V9, continuous
D76V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(15Q11.2) MUTATED      44                         4
  DEL PEAK 38(15Q11.2) WILD-TYPE    90                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 38(15Q11.2) MUTATED                                           0
  DEL PEAK 38(15Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 38(15Q11.2) MUTATED     111
  DEL PEAK 38(15Q11.2) WILD-TYPE   281
D76V11, multiclass
                                           clus
vv                                          DEL PEAK 38(15Q11.2) MUTATED
  ASIAN                                                               44
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              111
                                           clus
vv                                          DEL PEAK 38(15Q11.2) WILD-TYPE
  ASIAN                                                                 90
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                281
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 38(15Q11.2) MUTATED     2 117
  DEL PEAK 38(15Q11.2) WILD-TYPE   9 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(15Q11.2) MUTATED      2  117
  DEL PEAK 38(15Q11.2) WILD-TYPE    9  287
                        clus
vv                       DEL PEAK 38(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       DEL PEAK 38(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            287
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 39(16P13.3) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16P13.3) MUTATED    94  76
  DEL PEAK 39(16P13.3) WILD-TYPE 260 169
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                           170                            429 
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                            76                            169 
$`DEL PEAK 39(16P13.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       34.85        18.28         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-MX-A663 TCGA-VQ-A8PU TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.12         5.16         9.86        27.35        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
        5.92        13.94         8.94         4.21        32.45         7.69 
TCGA-IG-A3YC TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH 
       20.12        47.38        23.18        25.22         3.16        32.61 
TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        1.38         3.16        58.59         7.40         3.75         3.02 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       12.92        13.48         5.49        52.57        46.09        10.36 
TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A5U5 
       10.45        12.43        12.59        22.39        12.33         4.47 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.00        12.03        12.33        12.26         8.02         5.06 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       38.40         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE 
        2.30        12.69         7.00         5.29         3.42        16.44 
TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8Q7 TCGA-VR-AA7I 
        9.27        27.09        22.82        12.43        52.27        15.91 
TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-7197 TCGA-BR-7704 
        2.10         6.61        18.35         4.08         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 
       33.63        39.78         3.45        33.21        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-A4CQ 
       19.96        17.52        14.79        26.73        24.79        34.98 
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        13.35        11.21 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
       12.76        12.59        12.53        12.39        12.82         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4441 
       12.30        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        20.91 
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        20.32 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        19.96         7.99        72.23         0.56         5.52 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD 
       63.06         5.92        18.15        22.82         0.76        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RR 
       25.81        11.77        21.17         3.39        13.35         6.74 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       12.59        11.70        15.75         2.53         5.56        37.64 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 
       14.04        18.21         6.08         9.24        11.05        16.67 
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-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       43.36         7.73        46.26        22.19        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
        1.87        64.57        39.45         9.50        55.56         9.04 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54        66.81        21.04        42.54        43.66        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6J 
       17.13        27.55 

$`DEL PEAK 39(16P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39         4.31        19.99        22.82        35.97 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       20.02        47.05        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI 
        0.23        20.15        26.93        25.78        31.27        14.30 
TCGA-2H-A9GO TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
       16.24        33.27        35.21         0.85        20.78         2.63 
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-A8O2 TCGA-IG-A97H 
       23.41        12.82         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-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-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OP 
       26.33        21.01        47.93        18.35         3.32         7.17 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL 
       25.12        55.50         2.66        16.47        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L7-A56G 
        7.76        21.37         8.71        13.41        83.24        10.85 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25        12.62        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR 
       12.76        12.59        12.85        15.52        11.54        13.22 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.33        25.25        10.52        12.23        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-S8-A6BW TCGA-V5-AASV TCGA-V5-AASX 
        7.59        16.31         7.04        20.38        15.35         8.98 
TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       25.81         1.55        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR 
       18.18        46.19        18.05        11.24         9.17        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        41.23        14.37         3.42         1.32         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        9.47         9.44         6.97         4.64         7.43        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-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        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 
       44.94        21.90        36.16        35.84        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
       28.73         9.07        29.56        37.25        14.43        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.26        22.19         0.95        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        3.32        11.80        31.27         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       27.12         9.34        28.14         6.28         7.53        31.96 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       32.58         9.86        20.88         8.22        10.68        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       13.87         7.53         6.08        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 
        5.13        13.41        13.02        13.18        12.10         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.33        12.30        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.31         6.58        11.77        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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        4.01         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        15.02        28.96        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 
       21.07         7.99        25.71        12.66        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-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        12.36        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19        18.21        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.44        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        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-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        28.96        22.32        21.07        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.26        22.68        24.20         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        23.80        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       15.68        33.40        36.36         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
       12.46        19.53         6.44         6.51        10.62        13.51 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZF 
       63.62        36.95         3.72        19.73        45.67         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
       74.53         4.60         8.61         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       16.87        19.04         0.92        18.48        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF 
       38.14        37.22        30.97        34.29        16.31         2.50 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
       17.85         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       14.33        73.41        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y 
       20.81        32.88         1.71        42.64        60.85         9.73 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94T 
        2.01        55.43         6.58         5.72         2.66        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                          0.36                           0.00 
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE 
                        12.725                         14.500 
[1] "0.4 - 72.2 (12.7)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.2"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(16P13.3) MUTATED         4        9        9       11        19
  DEL PEAK 39(16P13.3) WILD-TYPE       6       12       38       22        68
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16P13.3) MUTATED          19        12         36         16
  DEL PEAK 39(16P13.3) WILD-TYPE        68        16         59         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 39(16P13.3) MUTATED            7       11         1
  DEL PEAK 39(16P13.3) WILD-TYPE         39       38         3
D77V3, multiclass
            clus
vv           DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              9                             12
  STAGE IB                              9                             38
  STAGE II                             11                             22
  STAGE IIA                            19                             68
  STAGE IIB                            19                             68
  STAGE III                            12                             16
  STAGE IIIA                           36                             59
  STAGE IIIB                           16                             56
  STAGE IIIC                            7                             39
  STAGE IV                             11                             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 39(16P13.3) MUTATED      20  30  88  23
  DEL PEAK 39(16P13.3) WILD-TYPE    35 106 195 101
D77V4, multiclass
       clus
vv      DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  T0+T1                           20                             35
  T2                              30                            106
  T3                              88                            195
  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 39(16P13.3) MUTATED    51  60  30  19
  DEL PEAK 39(16P13.3) WILD-TYPE 156 127  68  77
D77V5, multiclass
    clus
vv   DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  N0                           51                            156
  N1                           60                            127
  N2                           30                             68
  N3                           19                             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"
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(16P13.3) MUTATED   146   7
  DEL PEAK 39(16P13.3) WILD-TYPE 378  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16P13.3) MUTATED    146    7
  DEL PEAK 39(16P13.3) WILD-TYPE  378   32
   clus
vv  DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  0                          146                            378
  1                            7                             32
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16P13.3) MUTATED    40 137
  DEL PEAK 39(16P13.3) WILD-TYPE 145 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16P13.3) MUTATED     40  137
  DEL PEAK 39(16P13.3) WILD-TYPE  145  303
        clus
vv       DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  FEMALE                           40                            145
  MALE                            137                            303
[1] 2 2
[1] FALSE
D77V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(16P13.3) MUTATED   127  34
  DEL PEAK 39(16P13.3) WILD-TYPE 318  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16P13.3) MUTATED    127   34
  DEL PEAK 39(16P13.3) WILD-TYPE  318   85
     clus
vv    DEL PEAK 39(16P13.3) MUTATED DEL PEAK 39(16P13.3) WILD-TYPE
  NO                           127                            318
  YES                           34                             85
[1] 2 2
[1] FALSE
D77V9, continuous
D77V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(16P13.3) MUTATED      37                         6
  DEL PEAK 39(16P13.3) WILD-TYPE    97                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 39(16P13.3) MUTATED                                           0
  DEL PEAK 39(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 39(16P13.3) MUTATED     109
  DEL PEAK 39(16P13.3) WILD-TYPE   283
D77V11, multiclass
                                           clus
vv                                          DEL PEAK 39(16P13.3) MUTATED
  ASIAN                                                               37
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              109
                                           clus
vv                                          DEL PEAK 39(16P13.3) WILD-TYPE
  ASIAN                                                                 97
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                283
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 39(16P13.3) MUTATED     3 103
  DEL PEAK 39(16P13.3) WILD-TYPE   8 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16P13.3) MUTATED      3  103
  DEL PEAK 39(16P13.3) WILD-TYPE    8  301
                        clus
vv                       DEL PEAK 39(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       DEL PEAK 39(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            301
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 40(16P13.3) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(16P13.3) MUTATED    83  64
  DEL PEAK 40(16P13.3) WILD-TYPE 271 181
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                           147                            452 
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                            64                            181 
$`DEL PEAK 40(16P13.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NT 
       34.85        18.28        24.00         4.70         0.36        27.12 
TCGA-Q9-A6FU TCGA-CG-4444 TCGA-VQ-A8PU TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
        5.16        47.05        27.35        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3YC TCGA-JY-A6FH 
       13.94         8.94         4.21        32.45        20.12        47.38 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A4OS 
       23.18        25.22         3.16        32.61         3.16        58.59 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NN 
        7.40         3.75         3.02        12.92        13.48         5.49 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A4A5 
       52.57        10.36        10.45        12.43        12.59        22.39 
TCGA-LN-A4MQ TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.33        12.00        12.03        12.26         8.02         5.06 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         2.30        12.69         7.00 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
        5.29        16.44         9.27        27.09        22.82        12.43 
TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-Z6-A8JE TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-7197 
       52.27        15.91         2.10         6.61         4.08         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8286 
       35.24        33.63        39.78         3.45        33.21        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 
        2.66        19.96        17.52        14.79        26.73        24.79 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5802 
        7.53        34.98         1.48         0.72         1.15        13.35 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 
       11.21        12.76        12.59        12.53        12.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4449 
        6.31        12.30        12.43        11.61        12.20        19.07 
TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX 
       12.03        12.03        20.91        15.22        12.33        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8211 TCGA-HF-7133 
       22.29        19.96         7.99        72.23        13.58        63.06 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.92        18.15        22.82         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        23.80        21.17        33.40         3.39 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H 
       13.35         6.44         6.74        12.59         5.56        37.64 
TCGA-MX-A666 TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 
       14.04         6.08         9.24        11.05        16.67        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        46.26        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA68 
        1.87        64.57        55.56         9.04        21.04        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
       38.93        17.13        27.55 

$`DEL PEAK 40(16P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97        20.02        21.99        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23        20.15         9.86        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       14.30        16.24         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L 
       20.78         2.63        18.64         3.88         9.30         0.53 
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-A6F8 TCGA-JY-A6FA TCGA-JY-A6FD 
        4.67        14.50        12.16       122.10        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC 
        3.68        41.52        21.70        31.56        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        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-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NF 
        7.43        15.48         2.60        25.12        55.50         2.66 
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-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M 
       13.41        83.24        46.09        10.85         5.92        12.66 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       12.85        15.52        11.54        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 
       25.25        10.52        12.23        13.18        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18         0.13        12.03        12.85        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.59        16.31         7.04        38.40        53.95         2.89 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET 
       20.38         3.42        15.35         8.98        25.81         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        33.70        18.18        46.19 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        18.21        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 
       14.37         3.42         1.32         2.66        19.73        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        9.34         9.67         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       21.90        36.16        35.84        18.15        15.32        28.73 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        9.07        29.56        37.25        14.43        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       29.59         9.60        32.25         8.05         0.56         2.20 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       15.58         7.40         6.18        31.10        13.08         0.26 
TCGA-BR-8364 TCGA-BR-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-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        31.96        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        9.86        20.88         8.22        10.68        34.13        13.87 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        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        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8527 TCGA-CD-8528 
       13.02        13.15        13.18        12.10         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 
       12.30        12.59        11.64        15.39        12.07        12.43 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.31         6.58        11.77        12.62        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        29.98         0.00         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85        13.35        17.19        10.26        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       18.21        14.66        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       11.44        20.32        15.65         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62        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-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 
        1.51        24.39        28.96        22.32        21.07        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ 
        5.59        24.26        22.68        24.20         3.25        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.58        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26         2.10        12.95        29.00        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36         3.45        18.81        18.38        12.46        19.53 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95         3.72        19.73        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
        8.52        74.53         4.60         8.61         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        8.94        16.87        19.04         0.92        43.36        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       37.41        38.14        37.22        30.97        34.29        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       18.74        20.81        32.88         1.71        42.64        60.85 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.50         9.73         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
        5.72        66.81         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-AA6K 
       28.41        32.94        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.26         0.79 

  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                          0.36                           0.00 
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE 
                         12.79                          14.40 
[1] "0.4 - 72.2 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D78V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(16P13.3) MUTATED         4        6        8       10        17
  DEL PEAK 40(16P13.3) WILD-TYPE       6       15       39       23        70
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(16P13.3) MUTATED          19        12         33         12
  DEL PEAK 40(16P13.3) WILD-TYPE        68        16         62         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 40(16P13.3) MUTATED            8        8         1
  DEL PEAK 40(16P13.3) WILD-TYPE         38       41         3
D78V3, multiclass
            clus
vv           DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              6                             15
  STAGE IB                              8                             39
  STAGE II                             10                             23
  STAGE IIA                            17                             70
  STAGE IIB                            19                             68
  STAGE III                            12                             16
  STAGE IIIA                           33                             62
  STAGE IIIB                           12                             60
  STAGE IIIC                            8                             38
  STAGE IV                              8                             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 40(16P13.3) MUTATED      17  25  78  22
  DEL PEAK 40(16P13.3) WILD-TYPE    38 111 205 102
D78V4, multiclass
       clus
vv      DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  T0+T1                           17                             38
  T2                              25                            111
  T3                              78                            205
  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 40(16P13.3) MUTATED    45  57  20  18
  DEL PEAK 40(16P13.3) WILD-TYPE 162 130  78  78
D78V5, multiclass
    clus
vv   DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  N0                           45                            162
  N1                           57                            130
  N2                           20                             78
  N3                           18                             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"
D78V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(16P13.3) MUTATED   130   6
  DEL PEAK 40(16P13.3) WILD-TYPE 394  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(16P13.3) MUTATED    130    6
  DEL PEAK 40(16P13.3) WILD-TYPE  394   33
   clus
vv  DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  0                          130                            394
  1                            6                             33
[1] 2 2
[1] FALSE
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(16P13.3) MUTATED    36 117
  DEL PEAK 40(16P13.3) WILD-TYPE 149 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(16P13.3) MUTATED     36  117
  DEL PEAK 40(16P13.3) WILD-TYPE  149  323
        clus
vv       DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  FEMALE                           36                            149
  MALE                            117                            323
[1] 2 2
[1] FALSE
D78V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(16P13.3) MUTATED   111  31
  DEL PEAK 40(16P13.3) WILD-TYPE 334  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(16P13.3) MUTATED    111   31
  DEL PEAK 40(16P13.3) WILD-TYPE  334   88
     clus
vv    DEL PEAK 40(16P13.3) MUTATED DEL PEAK 40(16P13.3) WILD-TYPE
  NO                           111                            334
  YES                           31                             88
[1] 2 2
[1] FALSE
D78V9, continuous
D78V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(16P13.3) MUTATED      36                         6
  DEL PEAK 40(16P13.3) WILD-TYPE    98                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 40(16P13.3) MUTATED                                           0
  DEL PEAK 40(16P13.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 40(16P13.3) MUTATED      90
  DEL PEAK 40(16P13.3) WILD-TYPE   302
D78V11, multiclass
                                           clus
vv                                          DEL PEAK 40(16P13.3) MUTATED
  ASIAN                                                               36
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               90
                                           clus
vv                                          DEL PEAK 40(16P13.3) WILD-TYPE
  ASIAN                                                                 98
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                302
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 40(16P13.3) MUTATED     3  89
  DEL PEAK 40(16P13.3) WILD-TYPE   8 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(16P13.3) MUTATED      3   89
  DEL PEAK 40(16P13.3) WILD-TYPE    8  315
                        clus
vv                       DEL PEAK 40(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           89
                        clus
vv                       DEL PEAK 40(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            315
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 41(16Q23.1) MUTATION ANALYSIS
D79V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(16Q23.1) MUTATED   151 106
  DEL PEAK 41(16Q23.1) WILD-TYPE 203 139
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                           257                            342 
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                           106                            139 
$`DEL PEAK 41(16Q23.1) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y 
       60.39        34.85        18.28         8.94        24.00         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
       35.97        27.12        47.05        22.98        79.07        16.24 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GK TCGA-2H-A9GL 
       20.15         9.86        26.93        31.27         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3QL TCGA-IG-A3YC 
       13.94         8.94        16.24         4.21        35.21        20.12 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93C 
        3.88         0.53        14.50       122.10        47.38        23.18 
TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON 
       31.56        25.22         3.16        26.33        21.01        18.35 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NJ 
        2.60         3.75         3.02        55.50         2.66        16.47 
TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       13.22         7.76         5.49         8.71        13.41        83.24 
TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49V 
       46.09        10.85        10.36        10.45        13.41        12.59 
TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A7HV TCGA-LN-A7HW 
       13.25        12.59        12.33        13.22        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FQ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        13.18        12.85         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 
       16.31         6.35        53.95         9.30        15.78         2.89 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00         5.29        16.44         9.27 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-AAPN 
       25.81        27.09        22.82        25.08         3.42         2.66 
TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       19.73        58.03        26.70        11.70        19.56        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 
        9.44         6.61         6.97        18.35         4.08         4.08 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-7703 
        9.57        17.29        19.33        26.10        18.05        36.16 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 
       35.24        33.63        18.15        28.73         3.45        33.21 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44         0.69         9.60         0.56        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8372 
       19.96        31.10        13.08         0.26        17.52        31.27 
TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 
       14.79        25.18        26.73        24.79        32.58         8.22 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE 
       13.87         7.53        34.98         0.72        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        1.15        21.44        13.15        13.35        11.21        12.76 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A 
       12.53        12.39        12.07        12.82         6.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       11.61        12.20        15.95         7.99         8.05        54.08 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5723 TCGA-CG-5724 
       19.07        12.03         7.07        30.97       105.07        12.03 
TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6526 
       15.02        25.71        12.66        20.91        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        12.36        19.50        18.21        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       36.43        13.78        11.24        11.31        22.29        15.65 
TCGA-D7-A747 TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-FP-A9TM 
        8.38        72.23        14.07        22.29         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 
       77.29        63.06        30.51         1.51         5.92        18.15 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH 
       22.82         0.76         5.59        24.26        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H4 
        8.98         6.58        20.25         0.26         2.10        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       23.80        21.17        33.40         3.45        18.81        18.38 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       19.53         6.44         6.51        11.70        15.75        13.51 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS 
        5.56        63.62        37.64         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        39.45 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       21.83        61.22        32.88         1.71         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-AA68 
       55.56         9.04         4.54         5.72        42.54        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-ZQ-A9CR 
       38.93        17.13        54.12        26.04         0.79 

$`DEL PEAK 41(16Q23.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU 
       15.68         4.31         4.70        19.99        22.82         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GI 
       20.02        21.99         0.23        27.35        25.78        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA 
       58.55        32.45         7.69        33.27         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
        2.63        18.64         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96        14.86         4.67        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93F TCGA-KH-A6WC 
       68.02         3.68        41.52        21.70        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP 
       30.25         0.30        32.61        47.93         3.32         7.17 
TCGA-L5-A4OQ TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NH TCGA-L5-A8NI 
        1.38        15.48        25.12         7.40        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N 
       13.55        21.37        52.57         5.92        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y 
       12.33        13.38        13.15        15.35        12.62        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        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A8HZ 
       11.54         4.47        12.33        25.25        12.23        12.33 
TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-M9-A5M8 
       13.38        13.18         0.13        12.03        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
        7.82         7.04        38.40        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
        8.98        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-AA7B 
       33.70        18.18        52.27        46.19        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
        9.17        15.91        18.21        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4256 
        1.32         9.47         4.64         7.43        30.90         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        9.67         6.18         6.61        34.68        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6707 
       13.68        39.12         9.17        32.78        25.61        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 
       21.90         9.21        35.84        39.78        15.32         9.07 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       29.56        37.25        14.43        29.59        32.25         8.05 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8366 
        2.20        15.58         7.40         6.18        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8381 
       26.33         4.31        14.04         3.32        11.80         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
       25.05         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        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       31.96         9.86        20.88        10.68        34.13         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        1.48        27.55        28.57        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 
       16.14         5.13        13.41        13.02        13.18        12.10 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
       12.59         7.17        12.33        12.30        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI 
       15.39        12.43        12.30        11.31         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 
       12.62        20.02         3.02        27.02         1.02         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       14.01        29.98         0.00         9.01        18.97        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-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-D7-6518 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-D7-6527 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        15.98        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       17.19        14.66        21.14        20.91        16.44         5.92 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       14.76        26.43        11.44        20.32         4.34        19.96 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.99        14.47        21.27        11.38 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        19.53        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
        0.56        52.21        26.47        24.39        28.96        22.32 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       21.07        24.30        22.68        24.20         3.25        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H3 
       21.37        29.98         0.10         6.51        12.95        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       14.07        15.68        36.36         3.39        12.46        13.35 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A93J TCGA-MX-A5UG 
        6.74        12.59        10.62         2.53        36.95         3.72 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       19.73        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A804 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60         8.61         5.13       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA 
      115.69       116.38        71.38        57.44        16.87        19.04 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       13.25        18.48        43.36        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
       37.22        30.97        34.29        16.31         2.50         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        29.59        73.41        11.70 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       18.74        20.81        42.64        60.85         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94T TCGA-VQ-AA64 
        6.58        66.81        21.04         2.66        11.24        18.41 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       28.41        32.94        16.14        27.55        12.43        17.26 

  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                          0.26                           0.00 
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                         122.1                          122.3 
  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE 
                        13.510                         14.055 
[1] "0.3 - 122.1 (13.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D79V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(16Q23.1) MUTATED         5        8       19       17        31
  DEL PEAK 41(16Q23.1) WILD-TYPE       5       13       28       16        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(16Q23.1) MUTATED          39        15         45         22
  DEL PEAK 41(16Q23.1) WILD-TYPE        48        13         50         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 41(16Q23.1) MUTATED           23       13         3
  DEL PEAK 41(16Q23.1) WILD-TYPE         23       36         1
D79V3, multiclass
            clus
vv           DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                              8                             13
  STAGE IB                             19                             28
  STAGE II                             17                             16
  STAGE IIA                            31                             56
  STAGE IIB                            39                             48
  STAGE III                            15                             13
  STAGE IIIA                           45                             50
  STAGE IIIB                           22                             50
  STAGE IIIC                           23                             23
  STAGE IV                             13                             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(16Q23.1) MUTATED      25  56 123  46
  DEL PEAK 41(16Q23.1) WILD-TYPE    30  80 160  78
D79V4, multiclass
       clus
vv      DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  T0+T1                           25                             30
  T2                              56                             80
  T3                             123                            160
  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 41(16Q23.1) MUTATED    78  88  36  43
  DEL PEAK 41(16Q23.1) WILD-TYPE 129  99  62  53
D79V5, multiclass
    clus
vv   DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  N0                           78                            129
  N1                           88                             99
  N2                           36                             62
  N3                           43                             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(16Q23.1) MUTATED   225   9
  DEL PEAK 41(16Q23.1) WILD-TYPE 299  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(16Q23.1) MUTATED    225    9
  DEL PEAK 41(16Q23.1) WILD-TYPE  299   30
   clus
vv  DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  0                          225                            299
  1                            9                             30
[1] 2 2
[1] FALSE
D79V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(16Q23.1) MUTATED    68 197
  DEL PEAK 41(16Q23.1) WILD-TYPE 117 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(16Q23.1) MUTATED     68  197
  DEL PEAK 41(16Q23.1) WILD-TYPE  117  243
        clus
vv       DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  FEMALE                           68                            117
  MALE                            197                            243
[1] 2 2
[1] FALSE
D79V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(16Q23.1) MUTATED   196  49
  DEL PEAK 41(16Q23.1) WILD-TYPE 249  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(16Q23.1) MUTATED    196   49
  DEL PEAK 41(16Q23.1) WILD-TYPE  249   70
     clus
vv    DEL PEAK 41(16Q23.1) MUTATED DEL PEAK 41(16Q23.1) WILD-TYPE
  NO                           196                            249
  YES                           49                             70
[1] 2 2
[1] FALSE
D79V9, continuous
D79V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(16Q23.1) MUTATED      52                         6
  DEL PEAK 41(16Q23.1) WILD-TYPE    82                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 41(16Q23.1) MUTATED                                           0
  DEL PEAK 41(16Q23.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 41(16Q23.1) MUTATED     169
  DEL PEAK 41(16Q23.1) WILD-TYPE   223
D79V11, multiclass
                                           clus
vv                                          DEL PEAK 41(16Q23.1) MUTATED
  ASIAN                                                               52
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              169
                                           clus
vv                                          DEL PEAK 41(16Q23.1) WILD-TYPE
  ASIAN                                                                 82
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                                cls
clus                               0   1
  DEL PEAK 41(16Q23.1) MUTATED     6 157
  DEL PEAK 41(16Q23.1) WILD-TYPE   5 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(16Q23.1) MUTATED      6  157
  DEL PEAK 41(16Q23.1) WILD-TYPE    5  247
                        clus
vv                       DEL PEAK 41(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          157
                        clus
vv                       DEL PEAK 41(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            247
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 42(17P12) MUTATION ANALYSIS
D80V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 42(17P12) MUTATED   152 109
  DEL PEAK 42(17P12) WILD-TYPE 202 136
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                         261                          338 
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                         109                          136 
$`DEL PEAK 42(17P12) MUTATED`
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       60.39        34.85        18.28        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 
       35.97        27.12         5.16        20.02        47.05        79.07 
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
       16.24         0.23         9.86        27.35        26.93        25.78 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR 
        7.63         5.92        13.94         8.94         4.21        32.45 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A97H TCGA-JY-A6F8 
       18.64         3.88         0.79        23.41        14.50       122.10 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       47.38        31.56        25.22        30.25        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX 
        3.32         7.17         4.90        29.00         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.60         3.75        55.50        13.48        16.47        13.22 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A49K TCGA-LN-A49L 
        5.49         8.71        13.41        83.24         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A5U6 
       12.66        13.15        15.35        13.25        12.59        12.33 
TCGA-LN-A7HV TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW 
       10.52        13.18        12.33        12.85        33.11         7.82 
TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 
        7.59         5.06         7.04        38.40         9.30        15.78 
TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE TCGA-V5-AASW 
        2.30        12.69         7.00        20.38        16.44         9.27 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        27.09        22.82        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 
        8.12        18.18        46.19        11.24        18.21        25.08 
TCGA-XP-A8T8 TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TJ 
       14.37         2.66        19.73        58.03        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 
        9.44         6.61         9.67         6.18        17.29        19.33 
TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 
        9.17        12.16         9.21        35.24        33.63        28.73 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 
       33.21        11.44         0.69         9.60        29.42         2.66 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 
       19.96        15.58        31.10        13.08        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 
        5.39        25.18        24.79        32.58         9.86        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 
       13.87         7.53        34.98         1.48         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 
       20.65        20.42         1.15        13.02        13.15        12.76 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 
       12.59         7.17        12.33        12.30        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        6.31        11.31        12.43        11.61        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         7.99         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
       29.98        19.07         7.07        30.97        36.00         1.02 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       15.02         4.01        69.04        20.91        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-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 
       19.96         7.99        72.23        11.38        14.07        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 
       13.58         0.56         6.21        77.29        63.06        26.47 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH 
        1.51        18.15        28.96        22.82        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
        8.98         6.58         2.10        12.95        23.80        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP 
       36.36        18.81         3.39        18.38        13.35         6.44 
TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H 
       12.59        11.70        15.75         2.53         5.56        37.64 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BT 
       36.95        14.04        45.67        18.21         9.24         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.67       115.69         8.94         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PH 
       13.02        18.48        43.36         7.73        46.26        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70        17.85         1.87        13.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       73.41        18.74        20.81        42.64         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
       55.56         9.04         4.54        66.81        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        32.94        17.13        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$`DEL PEAK 42(17P12) WILD-TYPE`
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T TCGA-CG-4460 
       15.68         4.31         8.94        19.99        22.82        21.99 
TCGA-CG-4475 TCGA-KB-A93G TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GO 
       22.98        20.15        31.27        14.30        58.55        16.24 
TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        7.69        33.27        35.21         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A6QS 
       20.12         9.30         0.53        17.03        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       14.86         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C 
       41.52        21.70        23.18        24.03         6.28         3.16 
TCGA-L5-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OR 
        0.30        21.01        47.93        18.35         1.38         3.16 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
       58.59        15.48        25.12         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NK TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
       12.92        13.55         7.76        21.37        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.85        10.36        12.43        13.41        12.33        13.38 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.59        12.62        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        12.85        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8I0 
        4.47        25.25        12.00        12.23        12.03        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6L4 
       13.18         0.13        12.03        12.26         8.02        16.31 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
        6.35        53.95         2.89         5.29         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7D 
       25.81        28.11        33.70        52.27        18.05         9.17 
TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-B7-5816 
       15.91        41.23         3.42         2.10         1.32        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         9.34         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       34.68        15.95        13.87        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        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        44.94        21.90        36.16        35.84 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       39.78        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       37.25        14.43        29.59        32.25         8.05         0.56 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        7.36        25.05         3.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 
       26.73        31.96        20.88         8.22        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       27.55        28.57        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
       28.34         0.66        32.52         0.46        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
        5.13        13.41        13.18        13.35        11.21        12.10 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.53        12.39        12.59        11.64        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
       12.30         6.58        11.77        12.62        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       14.01        12.03         0.00         9.01        18.97        12.00 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        6.97         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 
       19.13        18.61        17.85        12.79        12.36        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 
       11.24        11.44        20.32        22.29         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        7.13         0.62        14.47        21.27         3.48        19.53 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB 
       22.29        59.54         5.03         5.52        52.21        30.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        24.26        22.68        24.20         3.25        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       29.00        23.84        21.17        14.07        15.68         3.45 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X 
       12.46        19.53         6.74         6.51        10.62        13.51 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       63.62         3.72        19.73         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.60        11.05         5.13       122.30        37.91        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-A8P3 
        5.79        48.79        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PO 
       30.97        34.29        16.31        22.19         2.50         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        29.59        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       61.22        32.88         1.71        60.85         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 
        6.58         5.72        21.04         2.66        42.54        28.41 
TCGA-VQ-AA6A TCGA-ZA-A8F6 
       38.93        17.26 

  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                        0.23                         0.00 
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                       122.1                        122.3 
  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE 
                      13.480                       14.285 
[1] "0.2 - 122.1 (13.5)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D80V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(17P12) MUTATED         6        8       21       16        33
  DEL PEAK 42(17P12) WILD-TYPE       4       13       26       17        54
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(17P12) MUTATED          38        15         38         34
  DEL PEAK 42(17P12) WILD-TYPE        49        13         57         38
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 42(17P12) MUTATED           17       21         1
  DEL PEAK 42(17P12) WILD-TYPE         29       28         3
D80V3, multiclass
            clus
vv           DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  STAGE I                             6                            4
  STAGE IA                            8                           13
  STAGE IB                           21                           26
  STAGE II                           16                           17
  STAGE IIA                          33                           54
  STAGE IIB                          38                           49
  STAGE III                          15                           13
  STAGE IIIA                         38                           57
  STAGE IIIB                         34                           38
  STAGE IIIC                         17                           29
  STAGE IV                           21                           28
  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(17P12) MUTATED      24  61 128  43
  DEL PEAK 42(17P12) WILD-TYPE    31  75 155  81
D80V4, multiclass
       clus
vv      DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  T0+T1                         24                           31
  T2                            61                           75
  T3                           128                          155
  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 42(17P12) MUTATED    85  82  46  39
  DEL PEAK 42(17P12) WILD-TYPE 122 105  52  57
D80V5, multiclass
    clus
vv   DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  N0                         85                          122
  N1                         82                          105
  N2                         46                           52
  N3                         39                           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"
D80V6, binary
                              cls
clus                             0   1
  DEL PEAK 42(17P12) MUTATED   222  13
  DEL PEAK 42(17P12) WILD-TYPE 302  26
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(17P12) MUTATED    222   13
  DEL PEAK 42(17P12) WILD-TYPE  302   26
   clus
vv  DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  0                        222                          302
  1                         13                           26
[1] 2 2
[1] FALSE
D80V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(17P12) MUTATED    65 202
  DEL PEAK 42(17P12) WILD-TYPE 120 238
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(17P12) MUTATED     65  202
  DEL PEAK 42(17P12) WILD-TYPE  120  238
        clus
vv       DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  FEMALE                         65                          120
  MALE                          202                          238
[1] 2 2
[1] FALSE
D80V8, binary
                              cls
clus                             0   1
  DEL PEAK 42(17P12) MUTATED   181  58
  DEL PEAK 42(17P12) WILD-TYPE 264  61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(17P12) MUTATED    181   58
  DEL PEAK 42(17P12) WILD-TYPE  264   61
     clus
vv    DEL PEAK 42(17P12) MUTATED DEL PEAK 42(17P12) WILD-TYPE
  NO                         181                          264
  YES                         58                           61
[1] 2 2
[1] FALSE
D80V9, continuous
D80V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(17P12) MUTATED      49                         6
  DEL PEAK 42(17P12) WILD-TYPE    85                        11
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 42(17P12) MUTATED                                           1   169
  DEL PEAK 42(17P12) WILD-TYPE                                         0   223
D80V11, multiclass
                                           clus
vv                                          DEL PEAK 42(17P12) MUTATED
  ASIAN                                                             49
  BLACK OR AFRICAN AMERICAN                                          6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            169
                                           clus
vv                                          DEL PEAK 42(17P12) WILD-TYPE
  ASIAN                                                               85
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                              cls
clus                             0   1
  DEL PEAK 42(17P12) MUTATED     6 150
  DEL PEAK 42(17P12) WILD-TYPE   5 254
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(17P12) MUTATED      6  150
  DEL PEAK 42(17P12) WILD-TYPE    5  254
                        clus
vv                       DEL PEAK 42(17P12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        150
                        clus
vv                       DEL PEAK 42(17P12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          254
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 43(17Q24.3) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(17Q24.3) MUTATED    58  39
  DEL PEAK 43(17Q24.3) WILD-TYPE 296 206
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                            97                            502 
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                            39                            206 
$`DEL PEAK 43(17Q24.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A88Y TCGA-L5-A8NG TCGA-Q9-A6FU TCGA-CG-4444 TCGA-EQ-A4SO 
       34.85         0.36        35.97         5.16        47.05        16.24 
TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A5S3 
        0.23         9.86        26.93         8.94         4.21        23.41 
TCGA-IG-A97H TCGA-JY-A6FD TCGA-L5-A4OH TCGA-L5-A4OR TCGA-L5-A88Z TCGA-L5-A891 
       14.50        68.02        32.61         3.16         7.40         3.75 
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-LN-A9FQ TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8EX TCGA-VR-A8Q7 
       12.85        15.35         8.98        22.82        28.11        52.27 
TCGA-X8-AAAR TCGA-Z6-AAPN TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 
       18.21         2.66        11.01         9.67        19.33         9.17 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-8361 
       35.24        33.63        33.21         0.69        19.96        31.10 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A452 
       14.79         3.72         9.21         9.86        13.87         7.53 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 
        0.72        13.51        20.65         1.15        21.44        12.76 
TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
       12.33        15.39        11.31        11.61        12.20        20.02 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-5579 
       54.08         4.01        14.01         7.07         4.01        20.91 
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        19.96 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-IN-8462 
        5.92        18.15        28.96         8.98        12.95        18.81 
TCGA-IN-8663 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
        3.39        37.64        45.67         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PH TCGA-VQ-A8PX 
        8.94         5.79         5.46        46.26        12.79        64.57 
TCGA-VQ-A91N TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA6I 
       18.74         9.50         9.73         4.54         5.72        16.14 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 43(17Q24.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE 
       15.68        60.39        18.28         4.31         8.94        24.00 
TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4460 
        4.70        19.99        22.82        27.12        20.02        21.99 
TCGA-CG-4475 TCGA-CG-5727 TCGA-KB-A93G TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH 
       22.98        79.07        20.15        27.35        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GO 
       14.30        58.55         7.63         5.92        13.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       32.45         7.69        33.27        35.21         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-A6FA TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16       122.10        44.75         3.68        41.52        47.38 
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-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        26.33        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-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
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-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NS 
       13.55        13.22         7.76         5.49        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       83.24        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        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        12.85        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-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP 
       12.23        12.33        13.38        13.18         0.13        12.03 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.26        33.11         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW 
       15.78         2.89         2.30        12.69         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP 
        5.29         3.42        16.44         9.27        25.81        27.09 
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        33.70        18.18 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       46.19        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-ZR-A9CJ 
       41.23        14.37         3.42         2.10         1.32        19.73 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        6.61         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        9.21        36.16        35.84        39.78        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        37.25        14.43 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       11.44        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       29.42         2.66         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-8381 
        4.31        14.04         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       25.05         5.39        25.18        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       24.79        31.96        32.58        20.88         8.22        10.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       34.13         6.08        34.98         1.48        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       32.52         0.46        20.42        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.59        12.53         7.17        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        12.07        12.82        12.43         6.31        12.30 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43         6.58        11.77        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 
       15.95         1.02         7.99         8.05        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01        18.97        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        15.02        28.96        65.10        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        13.35        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        18.21        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.44        20.32        22.29        15.65         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         0.62         7.99        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27        11.38         3.48        19.53        14.07        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       23.84        23.80        21.17        14.07        15.68        33.40 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       36.36         3.45        18.38        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        6.44         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       15.75        13.51         2.53         5.56        63.62        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV 
        6.08         4.60         9.24        11.05         5.13       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       37.91        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87        19.04         0.92        48.79        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       18.48        43.36        21.73        37.41        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF 
        7.73        30.97        34.29        16.31        22.19         2.50 
TCGA-VQ-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-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       13.35        29.59        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 
       60.85        55.56         9.04         2.01        55.43         6.58 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       43.66        28.41        38.93        32.94        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        27.55        12.43        17.26 

  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE 
                         12.85                          14.12 
[1] "0.2 - 115.7 (12.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D81V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(17Q24.3) MUTATED         1        2        2        3        16
  DEL PEAK 43(17Q24.3) WILD-TYPE       9       19       45       30        71
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(17Q24.3) MUTATED          13         6         19         15
  DEL PEAK 43(17Q24.3) WILD-TYPE        74        22         76         57
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 43(17Q24.3) MUTATED            7        9         1
  DEL PEAK 43(17Q24.3) WILD-TYPE         39       40         3
D81V3, multiclass
            clus
vv           DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              2                             19
  STAGE IB                              2                             45
  STAGE II                              3                             30
  STAGE IIA                            16                             71
  STAGE IIB                            13                             74
  STAGE III                             6                             22
  STAGE IIIA                           19                             76
  STAGE IIIB                           15                             57
  STAGE IIIC                            7                             39
  STAGE IV                              9                             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 43(17Q24.3) MUTATED       7  14  53  24
  DEL PEAK 43(17Q24.3) WILD-TYPE    48 122 230 100
D81V4, multiclass
       clus
vv      DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  T0+T1                            7                             48
  T2                              14                            122
  T3                              53                            230
  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 43(17Q24.3) MUTATED    30  27  22  17
  DEL PEAK 43(17Q24.3) WILD-TYPE 177 160  76  79
D81V5, multiclass
    clus
vv   DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  N0                           30                            177
  N1                           27                            160
  N2                           22                             76
  N3                           17                             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"
D81V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(17Q24.3) MUTATED    90   5
  DEL PEAK 43(17Q24.3) WILD-TYPE 434  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(17Q24.3) MUTATED     90    5
  DEL PEAK 43(17Q24.3) WILD-TYPE  434   34
   clus
vv  DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  0                           90                            434
  1                            5                             34
[1] 2 2
[1] FALSE
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(17Q24.3) MUTATED    34  69
  DEL PEAK 43(17Q24.3) WILD-TYPE 151 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(17Q24.3) MUTATED     34   69
  DEL PEAK 43(17Q24.3) WILD-TYPE  151  371
        clus
vv       DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  FEMALE                           34                            151
  MALE                             69                            371
[1] 2 2
[1] FALSE
D81V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(17Q24.3) MUTATED    73  11
  DEL PEAK 43(17Q24.3) WILD-TYPE 372 108
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(17Q24.3) MUTATED     73   11
  DEL PEAK 43(17Q24.3) WILD-TYPE  372  108
     clus
vv    DEL PEAK 43(17Q24.3) MUTATED DEL PEAK 43(17Q24.3) WILD-TYPE
  NO                            73                            372
  YES                           11                            108
[1] 2 2
[1] FALSE
D81V9, continuous
D81V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(17Q24.3) MUTATED      23                         1
  DEL PEAK 43(17Q24.3) WILD-TYPE   111                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 43(17Q24.3) MUTATED                                           1
  DEL PEAK 43(17Q24.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 43(17Q24.3) MUTATED      64
  DEL PEAK 43(17Q24.3) WILD-TYPE   328
D81V11, multiclass
                                           clus
vv                                          DEL PEAK 43(17Q24.3) MUTATED
  ASIAN                                                               23
  BLACK OR AFRICAN AMERICAN                                            1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               64
                                           clus
vv                                          DEL PEAK 43(17Q24.3) WILD-TYPE
  ASIAN                                                                111
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                328
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 43(17Q24.3) MUTATED     1  68
  DEL PEAK 43(17Q24.3) WILD-TYPE  10 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(17Q24.3) MUTATED      1   68
  DEL PEAK 43(17Q24.3) WILD-TYPE   10  336
                        clus
vv                       DEL PEAK 43(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 43(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            336
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 44(18Q12.2) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(18Q12.2) MUTATED   163 120
  DEL PEAK 44(18Q12.2) WILD-TYPE 191 125
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                           283                            316 
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                           120                            125 
$`DEL PEAK 44(18Q12.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-KB-A93G 
       27.12         5.16        20.02        47.05        22.98        20.15 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GN 
       27.35        26.93        25.78        31.27        58.55         8.94 
TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB 
       16.24         4.21        32.45         7.69         0.85         2.63 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H 
        3.88         0.53         0.79        23.41         9.96        14.50 
TCGA-IG-A97I TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D 
       12.16        68.02         3.68        47.38        23.18        31.56 
TCGA-JY-A93E TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH 
       25.22        24.03         3.16         0.30        26.33        32.61 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        3.32         7.17         3.16         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE 
        7.43        15.48         2.60         3.75         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-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G 
       21.37         8.71        13.41        83.24        52.57        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.36        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A4A1 TCGA-LN-A4A5 TCGA-LN-A4A6 
       13.38        15.35        13.25        12.59        22.39        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
       12.33        13.22         4.47        12.23        13.18        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN 
       13.18        12.03        12.85        33.11         7.82         8.02 
TCGA-R6-A6DQ TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        7.59         6.35        53.95         2.89         2.30        12.69 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-VR-A8EP TCGA-VR-A8EQ 
        7.00         5.29         3.42         9.27        27.09        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        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD 
        9.17        15.91        18.21        25.08        41.23         3.42 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
        2.66        19.73        58.03        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 
        9.47         9.44         6.61         4.08         6.18         9.57 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 
       17.29        13.68        26.10        12.16        35.24        33.63 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 
       15.32        28.73         3.45         9.07        11.44        29.42 
TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8486 
       19.96        22.19         0.95        14.04         3.32        20.22 
TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       27.12        26.73         9.86        20.88         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 
       13.87         7.53        34.98        12.89         0.66        13.51 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       21.44        13.02        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.76        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
       11.64        15.39        12.07         6.31        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-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        4.01        19.07        18.97         7.07        12.00        30.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 
        1.02        12.03         4.01        69.04        25.71        19.13 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.54        13.35        17.19        10.26        15.98 
TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
       12.33        19.50        18.21        14.66        21.14        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       16.44        36.43        11.24        20.32        22.29        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
       19.96         0.62         7.99        11.38        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 
       22.29        17.06        13.58         0.56         5.52        63.06 
TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 
        5.92        28.96        22.82        21.07        24.30        24.26 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        11.77         8.98         6.58         2.10        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR 
       23.84        21.17         3.45        18.38        13.35         6.74 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        13.51         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 
       37.64        45.67        18.21         8.52         6.08         9.24 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DL 
       16.67        37.91       115.69        35.61         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
       48.79         5.46        13.25        18.48        43.36         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91V TCGA-VQ-A91X 
       22.19         2.50        17.85        13.35        42.64         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R 
       55.56         9.04         2.01         4.54        66.81        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6K 
       11.24        18.41        38.93        32.94        26.04        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 44(18Q12.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GI 
       21.99        79.07        16.24         0.23         9.86        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YA 
        7.63         5.92        13.94        33.27        35.21        20.78 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 TCGA-IG-A7DP 
       20.12        18.64         9.30        17.03        12.82        14.86 
TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A939 TCGA-KH-A6WC 
        4.67       122.10        44.75        41.52        21.70         6.28 
TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
       30.25        21.01        47.93        18.35         1.38        58.59 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW TCGA-LN-A49K 
       25.12         7.40         7.76         5.49        46.09         5.92 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 
       13.15        12.59        12.62        12.46        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.59        15.52        11.54        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6KZ 
       12.00        12.03        12.33         0.13        12.26         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-S8-A6BW 
       16.31         7.04        38.40         9.30        15.78        20.38 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8ET TCGA-VR-A8EX 
       16.44        15.35         8.98        25.81         1.55        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA7B TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB 
       33.70        52.27        11.24        14.37         2.10         1.32 
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
       26.70         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        4.08         9.34         9.67         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        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
       18.15        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
       29.59         9.60        32.25         8.05         0.56         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        2.20        15.58         7.40         6.18        31.10        13.08 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
        0.26        17.52        26.33         4.31        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       14.79         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
        7.53        24.79        31.96        32.58        34.13         6.08 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34        32.52         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-8530 
        1.15        16.14         5.13        13.41        13.15        12.39 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
       12.59        12.82        12.43        12.30        11.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
       11.77        12.62        27.02        15.95         1.02        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5718 
       29.98        12.03         0.00         9.01         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-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       65.10        21.07         7.99        12.66        20.91        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        15.22        12.79        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY 
       24.72        16.80        17.19        20.91         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        11.31        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
        7.13        14.47        72.23        21.27         3.48        59.54 
TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.03         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G3 
        1.51        24.39        18.15        22.32         0.76         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 
        0.10         6.51        20.25         0.26        29.00        23.80 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40        36.36        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V 
       12.46        19.53         6.44        12.59         6.51        15.75 
TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A804 
       36.95         3.72        19.73        14.04        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         8.61         5.13       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DZ 
       71.38        57.44         8.94        16.87        19.04        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        37.41        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31        12.79         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 
       32.88         1.71        60.85         9.73        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D 
        5.72        21.04         2.66        43.66        28.41        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        16.14        27.55        17.26 

  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                           0.3                            0.0 
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE 
                         13.25                          15.55 
[1] "0.3 - 115.7 (13.2)" "0.0 - 122.3 (15.6)"
[1] "hr=" "1.2"
D82V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(18Q12.2) MUTATED         5        6       18       16        44
  DEL PEAK 44(18Q12.2) WILD-TYPE       5       15       29       17        43
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(18Q12.2) MUTATED          40        18         44         37
  DEL PEAK 44(18Q12.2) WILD-TYPE        47        10         51         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 44(18Q12.2) MUTATED           17       20         2
  DEL PEAK 44(18Q12.2) WILD-TYPE         29       29         2
D82V3, multiclass
            clus
vv           DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  STAGE I                               5                              5
  STAGE IA                              6                             15
  STAGE IB                             18                             29
  STAGE II                             16                             17
  STAGE IIA                            44                             43
  STAGE IIB                            40                             47
  STAGE III                            18                             10
  STAGE IIIA                           44                             51
  STAGE IIIB                           37                             35
  STAGE IIIC                           17                             29
  STAGE IV                             20                             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 44(18Q12.2) MUTATED      22  62 158  36
  DEL PEAK 44(18Q12.2) WILD-TYPE    33  74 125  88
D82V4, multiclass
       clus
vv      DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  T0+T1                           22                             33
  T2                              62                             74
  T3                             158                            125
  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 44(18Q12.2) MUTATED    93  89  48  42
  DEL PEAK 44(18Q12.2) WILD-TYPE 114  98  50  54
D82V5, multiclass
    clus
vv   DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  N0                           93                            114
  N1                           89                             98
  N2                           48                             50
  N3                           42                             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"
D82V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q12.2) MUTATED   241  17
  DEL PEAK 44(18Q12.2) WILD-TYPE 283  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q12.2) MUTATED    241   17
  DEL PEAK 44(18Q12.2) WILD-TYPE  283   22
   clus
vv  DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  0                          241                            283
  1                           17                             22
[1] 2 2
[1] FALSE
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q12.2) MUTATED    77 215
  DEL PEAK 44(18Q12.2) WILD-TYPE 108 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q12.2) MUTATED     77  215
  DEL PEAK 44(18Q12.2) WILD-TYPE  108  225
        clus
vv       DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  FEMALE                           77                            108
  MALE                            215                            225
[1] 2 2
[1] FALSE
D82V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q12.2) MUTATED   204  59
  DEL PEAK 44(18Q12.2) WILD-TYPE 241  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q12.2) MUTATED    204   59
  DEL PEAK 44(18Q12.2) WILD-TYPE  241   60
     clus
vv    DEL PEAK 44(18Q12.2) MUTATED DEL PEAK 44(18Q12.2) WILD-TYPE
  NO                           204                            241
  YES                           59                             60
[1] 2 2
[1] FALSE
D82V9, continuous
D82V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(18Q12.2) MUTATED      67                         6
  DEL PEAK 44(18Q12.2) WILD-TYPE    67                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(18Q12.2) MUTATED                                           0
  DEL PEAK 44(18Q12.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 44(18Q12.2) MUTATED     178
  DEL PEAK 44(18Q12.2) WILD-TYPE   214
D82V11, multiclass
                                           clus
vv                                          DEL PEAK 44(18Q12.2) MUTATED
  ASIAN                                                               67
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              178
                                           clus
vv                                          DEL PEAK 44(18Q12.2) WILD-TYPE
  ASIAN                                                                 67
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                                cls
clus                               0   1
  DEL PEAK 44(18Q12.2) MUTATED     7 174
  DEL PEAK 44(18Q12.2) WILD-TYPE   4 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(18Q12.2) MUTATED      7  174
  DEL PEAK 44(18Q12.2) WILD-TYPE    4  230
                        clus
vv                       DEL PEAK 44(18Q12.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       DEL PEAK 44(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            230
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 45(18Q21.2) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(18Q21.2) MUTATED   186 127
  DEL PEAK 45(18Q21.2) WILD-TYPE 168 118
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                           313                            286 
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                           127                            118 
$`DEL PEAK 45(18Q21.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A8NG 
       34.85        18.28         8.94        24.00         4.70        35.97 
TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO 
       27.12         5.16        20.02        47.05        22.98        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
        0.23        20.15        27.35        26.93        25.78        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       14.30        58.55         7.63        13.94         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS 
       32.45         7.69         0.85         2.63        18.64         3.88 
TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I 
        0.53         0.79        23.41         9.96        14.50        12.16 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E 
       68.02         3.68        47.38        23.18        31.56        25.22 
TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ 
       24.03         3.16         0.30        26.33        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 
       15.48         2.60         3.75         3.02        55.50         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NQ 
       12.92        13.48        16.47        13.55        13.22        21.37 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ 
        8.71        13.41        83.24        52.57        10.85        10.36 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R 
       10.45        12.66        12.43        13.41        12.33        13.38 
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        12.85        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HX TCGA-LN-A8I0 
       13.22         4.47        12.33        25.25        12.23        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW 
       13.18        12.03        12.85        12.26        33.11         7.82 
TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
        8.02         7.59        38.40         6.35        53.95         9.30 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        2.89         2.30        12.69         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU 
        9.27        25.81        27.09        22.82        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
        8.12        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       25.08        41.23        14.37         3.42         2.66        19.73 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       58.03        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
        6.61         4.08         6.18         9.57        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       19.33        26.10        12.16        35.24        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8286 
       15.32        28.73         3.45         9.07        11.44        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
        2.66        19.96         7.40        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8677 
        3.32         5.39        20.22         1.12        27.12        26.73 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       31.96         9.86        20.88         8.22        10.68        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 
        7.53        34.98         1.48        12.89         0.66        13.51 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       20.42        21.44        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       11.21        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 
       12.33        12.30        11.64        15.39        12.07         6.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       12.43        11.61        12.20         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
        8.05        54.08         4.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 
       30.97        36.00         1.02        12.03         4.01        69.04 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
       25.71        20.91        19.13        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       17.19        10.26        15.98        12.33        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
       18.21        14.66        21.14        14.27        16.44        36.43 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       11.24        20.32        22.29        15.65        19.96         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        7.99        11.38        19.53        14.07        22.29        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 
       13.58         0.56         5.52        63.06         5.92        28.96 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GH 
       22.82        21.07        24.30        24.26        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
        8.98         6.58         2.10        12.95        23.84        23.80 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP 
       21.17         3.45        18.81        18.38        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.74        10.62        11.70        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       63.62        37.64        45.67        18.21         8.52         6.08 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
        9.24        16.67        37.91       115.69        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        48.79        13.25        18.48        43.36        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PK TCGA-VQ-A8PS 
        7.73        16.31        22.19         2.50        17.85        13.35 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       61.22         1.71        42.64         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
        9.04         2.01         4.54        66.81        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6K 
       18.41        38.93        32.94        17.13        26.04        12.43 
TCGA-ZQ-A9CR 
        0.79 

$`DEL PEAK 45(18Q21.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y 
       15.68        60.39         4.31        19.99        22.82         0.36 
TCGA-CG-4460 TCGA-CG-5727 TCGA-MX-A663 TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IG-A3I8 
       21.99        79.07         9.86         5.92         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A625 
       35.21        20.78        20.12         9.30        17.03        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-JY-A6F8 TCGA-JY-A6FA TCGA-JY-A6FG TCGA-JY-A939 
       14.86         4.67       122.10        44.75        41.52        21.70 
TCGA-KH-A6WC TCGA-L5-A43E TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OQ TCGA-L5-A4OS 
        6.28        30.25        47.93        18.35         1.38        58.59 
TCGA-L5-A4OW TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NW 
        7.13        25.12         7.40         7.76         5.49        46.09 
TCGA-LN-A49K TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A2 
        5.92        13.15        15.35        12.59        12.62        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A7HV TCGA-LN-A7HW 
       12.76        12.59        15.52        11.54        10.52        12.00 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO TCGA-R6-A6KZ TCGA-R6-A6L4 
       12.03        13.18        12.33         0.13         5.06        16.31 
TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX 
        7.04        15.78        20.38         3.42        15.35         8.98 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        1.55        28.11        33.70        18.18        52.27        11.24 
TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        2.10         1.32        26.70         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 
       18.35        30.90         4.08         9.34         9.67         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       34.68        15.95        13.87        39.12         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        40.21        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       31.20        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
       18.15        29.56        33.21        37.25        14.43         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
       29.59         9.60        32.25         8.05         0.56         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 
       15.58         6.18        31.10        13.08         0.26        17.52 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       26.33         4.31        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8590 
       25.05         3.72        25.18         9.21        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-A44T 
       28.14         6.28         7.53        24.79        32.58        34.13 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF 
        0.53        28.34        32.52         0.46        20.65         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
       16.14         5.13        13.41        12.39        12.59        12.82 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.43        12.30        11.31         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       20.02        15.95         1.02        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       12.03         0.00         9.01         6.97         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 
        7.99        12.66        18.84        18.61        17.85        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 
       12.79        12.36        11.31        16.80        17.19        20.91 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        13.78        14.76        26.43        11.31        11.44 
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-8209 TCGA-FP-8210 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
        3.48        59.54         5.03         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        18.15        22.32 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        0.76         5.59        22.68        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        20.25         0.26 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8663 
       29.00        14.07        15.68        33.40        36.36         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93J 
       12.46        19.53        12.59         6.51        15.75        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS 
        3.72        19.73        14.04        74.53         4.60        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        8.61         5.13       122.30        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       57.44         8.94        16.87        19.04         5.46        13.02 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       37.41        38.14        37.22        30.97        34.29        46.26 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       12.79         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       29.59        64.57        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A924 
       21.83        18.74        20.81        32.88        60.85        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        43.66        28.41 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       54.12        16.14        27.55        17.26 

  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                        115.69                         122.30 
  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE 
                        13.350                         15.285 
[1] "0.2 - 115.7 (13.3)" "0.0 - 122.3 (15.3)"
[1] "hr=" "1.1"
D83V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(18Q21.2) MUTATED         6        6       22       17        47
  DEL PEAK 45(18Q21.2) WILD-TYPE       4       15       25       16        40
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(18Q21.2) MUTATED          47        19         48         38
  DEL PEAK 45(18Q21.2) WILD-TYPE        40         9         47         34
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 45(18Q21.2) MUTATED           22       22         2
  DEL PEAK 45(18Q21.2) WILD-TYPE         24       27         2
D83V3, multiclass
            clus
vv           DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  STAGE I                               6                              4
  STAGE IA                              6                             15
  STAGE IB                             22                             25
  STAGE II                             17                             16
  STAGE IIA                            47                             40
  STAGE IIB                            47                             40
  STAGE III                            19                              9
  STAGE IIIA                           48                             47
  STAGE IIIB                           38                             34
  STAGE IIIC                           22                             24
  STAGE IV                             22                             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
  DEL PEAK 45(18Q21.2) MUTATED      27  69 167  45
  DEL PEAK 45(18Q21.2) WILD-TYPE    28  67 116  79
D83V4, multiclass
       clus
vv      DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  T0+T1                           27                             28
  T2                              69                             67
  T3                             167                            116
  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 45(18Q21.2) MUTATED   102 101  49  49
  DEL PEAK 45(18Q21.2) WILD-TYPE 105  86  49  47
D83V5, multiclass
    clus
vv   DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  N0                          102                            105
  N1                          101                             86
  N2                           49                             49
  N3                           49                             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(18Q21.2) MUTATED   267  19
  DEL PEAK 45(18Q21.2) WILD-TYPE 257  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(18Q21.2) MUTATED    267   19
  DEL PEAK 45(18Q21.2) WILD-TYPE  257   20
   clus
vv  DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  0                          267                            257
  1                           19                             20
[1] 2 2
[1] FALSE
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(18Q21.2) MUTATED    85 238
  DEL PEAK 45(18Q21.2) WILD-TYPE 100 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(18Q21.2) MUTATED     85  238
  DEL PEAK 45(18Q21.2) WILD-TYPE  100  202
        clus
vv       DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  FEMALE                           85                            100
  MALE                            238                            202
[1] 2 2
[1] FALSE
D83V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(18Q21.2) MUTATED   225  67
  DEL PEAK 45(18Q21.2) WILD-TYPE 220  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(18Q21.2) MUTATED    225   67
  DEL PEAK 45(18Q21.2) WILD-TYPE  220   52
     clus
vv    DEL PEAK 45(18Q21.2) MUTATED DEL PEAK 45(18Q21.2) WILD-TYPE
  NO                           225                            220
  YES                           67                             52
[1] 2 2
[1] FALSE
D83V9, continuous
D83V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(18Q21.2) MUTATED      73                         6
  DEL PEAK 45(18Q21.2) WILD-TYPE    61                        11
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 45(18Q21.2) MUTATED                                           0
  DEL PEAK 45(18Q21.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 45(18Q21.2) MUTATED     201
  DEL PEAK 45(18Q21.2) WILD-TYPE   191
D83V11, multiclass
                                           clus
vv                                          DEL PEAK 45(18Q21.2) MUTATED
  ASIAN                                                               73
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              201
                                           clus
vv                                          DEL PEAK 45(18Q21.2) WILD-TYPE
  ASIAN                                                                 61
  BLACK OR AFRICAN AMERICAN                                             11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, binary
                                cls
clus                               0   1
  DEL PEAK 45(18Q21.2) MUTATED     9 196
  DEL PEAK 45(18Q21.2) WILD-TYPE   2 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(18Q21.2) MUTATED      9  196
  DEL PEAK 45(18Q21.2) WILD-TYPE    2  208
                        clus
vv                       DEL PEAK 45(18Q21.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          196
                        clus
vv                       DEL PEAK 45(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            208
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 46(19P13.3) MUTATION ANALYSIS
D84V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(19P13.3) MUTATED   136 104
  DEL PEAK 46(19P13.3) WILD-TYPE 218 141
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                           240                            359 
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                           104                            141 
$`DEL PEAK 46(19P13.3) MUTATED`
TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A8NG TCGA-CG-4460 TCGA-CG-4475 TCGA-KB-A93G 
        4.31        24.00        35.97        21.99        22.98        20.15 
TCGA-VQ-A8PU TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       27.35        25.78        31.27        14.30        58.55         7.63 
TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3YB TCGA-IG-A4QS 
       13.94         8.94        16.24         4.21         2.63         3.88 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-JY-A6FA 
        0.53        17.03         0.79        23.41         4.67        44.75 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH 
       68.02        47.38        23.18        30.25        26.33        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OX 
       47.93         3.32         7.17         1.38        58.59         7.43 
TCGA-L5-A88V TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK 
        2.60         3.75         2.66        12.92        16.47        13.55 
TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G 
        5.49         8.71        13.41        52.57        46.09        10.85 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       10.36        10.45        12.66        13.38        13.15        15.35 
TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A6 TCGA-LN-A4MQ 
       13.25        12.46        12.49        12.76        12.85        12.33 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HV TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8I0 
        4.47        12.33        10.52        12.23        13.18        13.38 
TCGA-LN-A9FO TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        0.13        12.26         8.02         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
        6.35        53.95        15.78         2.89         2.30        12.69 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        3.42        16.44         9.27        25.81        27.09        12.43 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-Z6-A8JE 
        8.12        52.27        46.19         9.17        25.08         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.66        19.73        58.03        19.56        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4257 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
        6.61         9.67        19.33         9.17         9.21        35.24 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 
       39.78        28.73         3.45        11.44         0.69        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8485 
        2.66        19.96         2.20        14.04        14.79         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       20.22        24.79        10.68        34.98         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.72        20.65         1.15        13.02        13.15        13.35 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       12.10        12.76        12.59        12.53         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.39        15.39        12.82         6.31        12.30        11.31 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 
       12.43        11.61        12.20        20.02         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5724 
        4.01        29.98        19.07        18.97        36.00        12.03 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6525 
       15.02         4.01        69.04        12.66        18.84        13.35 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8578 
       15.98        12.79        12.36        11.31        19.50        21.14 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 
       22.29        15.65         7.99        72.23        11.38        14.07 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 
       17.06         0.56         6.21        63.06         5.92        18.15 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       11.77         8.98         6.58         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       23.80        21.17        33.40        36.36        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38        13.35         6.74        12.59        10.62        11.70 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 
        2.53         5.56        63.62        37.64        36.95        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW 
       45.67        18.21         6.08         9.24         8.61         5.13 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       37.91         8.94         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 
       13.25        13.02        18.48        43.36        37.41         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91U 
       22.19        12.79         2.70        17.85         1.87         1.71 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       42.64         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        4.54         5.72        21.04        18.41        43.66        38.93 
TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        26.04        16.14        27.55        12.43         0.79 

$`DEL PEAK 46(19P13.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG 
       15.68        60.39        34.85        18.28         8.94         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV 
       19.99        22.82         0.36        27.12         5.16        20.02 
TCGA-CG-4444 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-VQ-A94U 
       47.05        79.07        16.24         0.23         9.86        26.93 
TCGA-2H-A9GL TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        5.92        32.45         7.69        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A625 TCGA-IG-A6QS 
       20.78        20.12        18.64         9.30        12.82         9.96 
TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86        14.50        12.16       122.10         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-A43H TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
        0.30        21.01        18.35         3.16         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
        7.13        15.48        25.12         7.40         3.02        55.50 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49K 
       13.48        13.22         7.76        21.37        83.24         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 
       12.43        13.41        12.33        12.59        12.62        12.59 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 
       12.59        22.39        15.52        11.54        13.22        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.00        12.03        12.33        13.18        12.03        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y2 TCGA-RE-A7BO 
       33.11         7.82         7.59        16.31         9.30         7.00 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-A8ET 
       20.38         5.29        15.35         8.98        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        33.70        18.18        18.05        11.24 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21        41.23        14.37         3.42         1.32 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       26.70        11.70         9.47         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
       18.35        30.90         4.08         4.08         9.34         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.87        17.29 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       13.68        39.12        26.10        32.78        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       19.89        12.16         8.98        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
       44.94        21.90        36.16        35.84        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         9.07        29.56        33.21        37.25        14.43 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8296 
       29.59         9.60        32.25         8.05         0.56        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27         7.36        25.05         3.72         5.39        25.18 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        31.96        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        8.22        34.13        13.87         7.53         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       28.57         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
       32.52        13.51         0.46        20.42        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8528 TCGA-CD-8531 
        5.13        13.41        13.18        11.21        12.33        12.59 
TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       11.64        12.07        12.43         6.58        11.77        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 
        3.02        27.02        15.95         1.02         8.05        14.01 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03         0.00         9.01         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
       28.96        65.10        21.07         7.99        25.71        20.91 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       19.13        20.55        18.54        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       10.26        15.22        12.33        24.72        16.80        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       18.21        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 
       36.43        13.78        14.76        26.43        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44        20.32         8.38         4.34        19.96         7.13 
TCGA-EQ-5647 TCGA-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-8211 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 
       59.54         5.03        13.58         5.52        77.29        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         1.51        24.39        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       22.68        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
       14.07        15.68         3.45        12.46        19.53         6.44 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZF 
        6.51        15.75        13.51         3.72        19.73         8.52 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       74.53         4.60        11.05        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       19.04        21.73        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       13.35        29.59        64.57        14.33        73.41        39.45 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-A94R 
       60.85        55.43         6.58        66.81         2.66        42.54 
TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-ZA-A8F6 
       11.24        28.41        32.94        54.12        17.26 

  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                         72.23                         122.30 
  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE 
                        12.805                         15.680 
[1] "0.1 - 72.2 (12.8)"  "0.0 - 122.3 (15.7)"
[1] "hr=" "1.3"
D84V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(19P13.3) MUTATED         4        8       17       14        30
  DEL PEAK 46(19P13.3) WILD-TYPE       6       13       30       19        57
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(19P13.3) MUTATED          39        16         36         26
  DEL PEAK 46(19P13.3) WILD-TYPE        48        12         59         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 46(19P13.3) MUTATED           17       19         3
  DEL PEAK 46(19P13.3) WILD-TYPE         29       30         1
D84V3, multiclass
            clus
vv           DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  STAGE I                               4                              6
  STAGE IA                              8                             13
  STAGE IB                             17                             30
  STAGE II                             14                             19
  STAGE IIA                            30                             57
  STAGE IIB                            39                             48
  STAGE III                            16                             12
  STAGE IIIA                           36                             59
  STAGE IIIB                           26                             46
  STAGE IIIC                           17                             29
  STAGE IV                             19                             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 46(19P13.3) MUTATED      21  53 123  36
  DEL PEAK 46(19P13.3) WILD-TYPE    34  83 160  88
D84V4, multiclass
       clus
vv      DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  T0+T1                           21                             34
  T2                              53                             83
  T3                             123                            160
  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 46(19P13.3) MUTATED    74  81  36  38
  DEL PEAK 46(19P13.3) WILD-TYPE 133 106  62  58
D84V5, multiclass
    clus
vv   DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  N0                           74                            133
  N1                           81                            106
  N2                           36                             62
  N3                           38                             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 46(19P13.3) MUTATED   203  15
  DEL PEAK 46(19P13.3) WILD-TYPE 321  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(19P13.3) MUTATED    203   15
  DEL PEAK 46(19P13.3) WILD-TYPE  321   24
   clus
vv  DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  0                          203                            321
  1                           15                             24
[1] 2 2
[1] FALSE
D84V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(19P13.3) MUTATED    55 194
  DEL PEAK 46(19P13.3) WILD-TYPE 130 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(19P13.3) MUTATED     55  194
  DEL PEAK 46(19P13.3) WILD-TYPE  130  246
        clus
vv       DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  FEMALE                           55                            130
  MALE                            194                            246
[1] 2 2
[1] FALSE
D84V8, binary
                                cls
clus                               0   1
  DEL PEAK 46(19P13.3) MUTATED   169  54
  DEL PEAK 46(19P13.3) WILD-TYPE 276  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(19P13.3) MUTATED    169   54
  DEL PEAK 46(19P13.3) WILD-TYPE  276   65
     clus
vv    DEL PEAK 46(19P13.3) MUTATED DEL PEAK 46(19P13.3) WILD-TYPE
  NO                           169                            276
  YES                           54                             65
[1] 2 2
[1] FALSE
D84V9, continuous
D84V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(19P13.3) MUTATED      62                         9
  DEL PEAK 46(19P13.3) WILD-TYPE    72                         8
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 46(19P13.3) MUTATED                                           1
  DEL PEAK 46(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 46(19P13.3) MUTATED     140
  DEL PEAK 46(19P13.3) WILD-TYPE   252
D84V11, multiclass
                                           clus
vv                                          DEL PEAK 46(19P13.3) MUTATED
  ASIAN                                                               62
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              140
                                           clus
vv                                          DEL PEAK 46(19P13.3) WILD-TYPE
  ASIAN                                                                 72
  BLACK OR AFRICAN AMERICAN                                              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                252
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, binary
                                cls
clus                               0   1
  DEL PEAK 46(19P13.3) MUTATED     4 145
  DEL PEAK 46(19P13.3) WILD-TYPE   7 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(19P13.3) MUTATED      4  145
  DEL PEAK 46(19P13.3) WILD-TYPE    7  259
                        clus
vv                       DEL PEAK 46(19P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 46(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            259
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 47(20P12.1) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(20P12.1) MUTATED    40  30
  DEL PEAK 47(20P12.1) WILD-TYPE 314 215
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            70                            529 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            30                            215 
$`DEL PEAK 47(20P12.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-EQ-A4SO TCGA-2H-A9GI TCGA-IG-A4QS TCGA-JY-A6FA 
       34.85         8.94        16.24        14.30         3.88        44.75 
TCGA-JY-A6FD TCGA-JY-A6FH TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A8NE 
       68.02        47.38        26.33        32.61         3.32        55.50 
TCGA-L5-A8NF TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
        2.66        16.47        13.22         8.71        13.41        83.24 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49Y TCGA-LN-A7HW 
       10.36        10.45        12.66        13.41        12.46        12.00 
TCGA-LN-A7HY TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW 
       12.03         5.06        38.40        53.95        12.69        20.38 
TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-XP-A8T8 TCGA-ZR-A9CJ TCGA-BR-4267 TCGA-BR-6456 
       22.82        52.27        14.37        19.73         6.18        17.29 
TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8289 TCGA-BR-A4IY TCGA-BR-A4PD TCGA-BR-A4QI 
       26.10        28.73         2.66        12.89        20.65        21.44 
TCGA-CD-8525 TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-5717 TCGA-CG-5725 TCGA-D7-6519 
       12.59        11.61         3.02         6.97        15.02        20.55 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8575 TCGA-D7-8576 TCGA-EQ-5647 TCGA-HF-7133 
       17.19        10.26        18.21        14.66         0.62        63.06 
TCGA-HU-8249 TCGA-HU-A4GF TCGA-IN-A6RJ TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A93J 
       28.96        25.81        12.46        15.75         2.53        36.95 
TCGA-RD-A8MW TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8P3 TCGA-VQ-A8PC 
       37.91        19.04         5.46        18.48        37.22        46.26 
TCGA-VQ-A8PK TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6D 
       17.85         4.54        43.66        17.13 

$`DEL PEAK 47(20P12.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG 
       15.68        60.39        18.28         4.31        24.00         4.70 
TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU 
       19.99        22.82         0.36        35.97        27.12         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX 
       20.02        47.05        21.99        22.98        79.07         0.23 
TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH 
       20.15         9.86        27.35        26.93        25.78        31.27 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         7.63         5.92        13.94         8.94        16.24 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        4.21        32.45         7.69        33.27        35.21         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-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-A6F8 TCGA-JY-A6FE TCGA-JY-A6FG 
        4.67        14.50        12.16       122.10         3.68        41.52 
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-A43H TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
        3.16        30.25         0.30        21.01        47.93        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
        7.13         7.43        15.48         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NM 
        3.75         3.02        12.92        13.48        13.55         7.76 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-LN-A49K 
        5.49        21.37        52.57        46.09        10.85         5.92 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       12.43        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       13.25        12.62        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        12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 
       12.26        33.11         7.82         8.02         7.59        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04         6.35         9.30        15.78         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-V5-AASW 
        7.00         5.29         3.42        16.44        15.35         9.27 
TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        8.98        25.81        27.09        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        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 
       11.24         9.17        15.91        18.21        25.08        41.23 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-3M-AB46 TCGA-B7-5816 
        3.42         2.10         1.32         2.66        58.03        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-4253 
        6.97         4.64         7.43        18.35        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         9.67         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.87        13.68        19.33        39.12         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       14.43        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42        19.96         2.20        15.58 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        31.10        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       11.80        31.27        14.79         7.36        25.05         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39        25.18         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       27.12         9.34        28.14         6.28         7.53        26.73 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       24.79        31.96        32.58         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        34.13        13.87         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        1.48        27.55        28.57         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        16.14         5.13        13.41        13.02 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 
       13.15        13.18        13.35        11.21        12.10        12.76 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       12.53         7.17        12.33        12.30        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       11.64        15.39        12.07        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.30        11.31        12.43         6.58        12.20        11.77 
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-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         0.00         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-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-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        25.71        12.66        20.91        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44        20.32        22.29        15.65 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34        19.96         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       14.07        15.68        33.40        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        13.35        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A6F5 
       12.59         6.51        10.62        11.70        13.51         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 
       63.62        37.64         3.72        19.73        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-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 
       43.36        21.73        37.41        38.14         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       34.29        16.31        22.19         2.50        12.79         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        1.87         9.27        23.41        15.65        13.35        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        73.41        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 
       60.85         9.50         9.73        55.56         9.04         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         6.58         5.72        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        18.41        28.41        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                          0.62                           0.00 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                         83.24                         122.30 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                        16.355                         13.550 
[1] "0.6 - 83.2 (16.4)"  "0.0 - 122.3 (13.6)"
[1] "hr=" "1.1"
D85V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(20P12.1) MUTATED         1        3        5        3         9
  DEL PEAK 47(20P12.1) WILD-TYPE       9       18       42       30        78
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(20P12.1) MUTATED          11         6         12          7
  DEL PEAK 47(20P12.1) WILD-TYPE        76        22         83         65
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 47(20P12.1) MUTATED            4        4         1
  DEL PEAK 47(20P12.1) WILD-TYPE         42       45         3
D85V3, multiclass
            clus
vv           DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  STAGE I                               1                              9
  STAGE IA                              3                             18
  STAGE IB                              5                             42
  STAGE II                              3                             30
  STAGE IIA                             9                             78
  STAGE IIB                            11                             76
  STAGE III                             6                             22
  STAGE IIIA                           12                             83
  STAGE IIIB                            7                             65
  STAGE IIIC                            4                             42
  STAGE IV                              4                             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 47(20P12.1) MUTATED       7  17  35   9
  DEL PEAK 47(20P12.1) WILD-TYPE    48 119 248 115
D85V4, multiclass
       clus
vv      DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  T0+T1                            7                             48
  T2                              17                            119
  T3                              35                            248
  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 47(20P12.1) MUTATED    23  24  11  10
  DEL PEAK 47(20P12.1) WILD-TYPE 184 163  87  86
D85V5, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  N0                           23                            184
  N1                           24                            163
  N2                           11                             87
  N3                           10                             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"
D85V6, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    56   4
  DEL PEAK 47(20P12.1) WILD-TYPE 468  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     56    4
  DEL PEAK 47(20P12.1) WILD-TYPE  468   35
   clus
vv  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  0                           56                            468
  1                            4                             35
[1] 2 2
[1] FALSE
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    19  53
  DEL PEAK 47(20P12.1) WILD-TYPE 166 387
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     19   53
  DEL PEAK 47(20P12.1) WILD-TYPE  166  387
        clus
vv       DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  FEMALE                           19                            166
  MALE                             53                            387
[1] 2 2
[1] FALSE
D85V8, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED    47  20
  DEL PEAK 47(20P12.1) WILD-TYPE 398  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED     47   20
  DEL PEAK 47(20P12.1) WILD-TYPE  398   99
     clus
vv    DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  NO                            47                            398
  YES                           20                             99
[1] 2 2
[1] FALSE
D85V9, continuous
D85V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(20P12.1) MUTATED      14                         2
  DEL PEAK 47(20P12.1) WILD-TYPE   120                        15
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 47(20P12.1) MUTATED                                           0
  DEL PEAK 47(20P12.1) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 47(20P12.1) MUTATED      47
  DEL PEAK 47(20P12.1) WILD-TYPE   345
D85V11, multiclass
                                           clus
vv                                          DEL PEAK 47(20P12.1) MUTATED
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                            2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               47
                                           clus
vv                                          DEL PEAK 47(20P12.1) WILD-TYPE
  ASIAN                                                                120
  BLACK OR AFRICAN AMERICAN                                             15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                345
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     2  38
  DEL PEAK 47(20P12.1) WILD-TYPE   9 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      2   38
  DEL PEAK 47(20P12.1) WILD-TYPE    9  366
                        clus
vv                       DEL PEAK 47(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       DEL PEAK 47(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            366
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 48(21Q11.2) MUTATION ANALYSIS
D86V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(21Q11.2) MUTATED   161 117
  DEL PEAK 48(21Q11.2) WILD-TYPE 193 128
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           278                            321 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                           117                            128 
$`DEL PEAK 48(21Q11.2) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       27.12        47.05        22.98         0.23        20.15         9.86 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       27.35        26.93        25.78         7.63         5.92        13.94 
TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 
       32.45        33.27         0.85        20.78        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-IG-A97I TCGA-JY-A6F8 
        3.88         0.53         0.79         9.96        12.16       122.10 
TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93F TCGA-L5-A43C TCGA-L5-A43E 
       68.02        23.18        31.56        24.03         3.16        30.25 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
        0.30        26.33        32.61        47.93        18.35         7.17 
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        15.48 
TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NF TCGA-L5-A8NH 
        2.60         7.40         3.75         3.02         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       16.47        13.55        13.22         5.49         8.71        13.41 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49N 
       52.57        46.09        10.85        10.36         5.92        12.43 
TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 
       13.41        13.38        13.15        13.25        12.62        12.76 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       22.39        12.85        11.54        13.22         4.47        12.33 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FQ 
       12.00        12.23        12.03        13.18        13.38        12.85 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         7.82         8.02         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-S8-A6BW 
        6.35         9.30         2.89         2.30        12.69        20.38 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ET 
       16.44         9.27         8.98        25.81        22.82         1.55 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA7B TCGA-XP-A8T7 
        8.12        28.11        52.27        46.19        11.24        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ 
       14.37         2.10         2.66        19.73        11.70        11.01 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 
        9.44         6.97         4.08         9.67        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       26.10         9.17        31.20        35.24        33.63        39.78 
TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 
       28.73        33.21        11.44        29.59         9.60         8.05 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8373 
       19.96        31.10        17.52         4.31        14.04        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 
        5.39        25.18         9.21        20.22        24.79         9.86 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       20.88         8.22        10.68         7.53        34.98         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.72        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       21.44        12.10        12.76        12.53         7.17        12.39 
TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       12.82        12.30        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 
       20.02        54.08         4.01        12.03        18.97        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 
       20.91        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-A9TM TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 
        5.52         6.21        63.06        26.47         1.51        28.96 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H3 
       22.82        22.68         3.25         8.98         0.26        29.00 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       23.80        21.17        33.40        36.36        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU 
       18.38        12.46        13.35         6.74        10.62        11.70 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
       15.75         2.53         5.56        63.62        37.64        36.95 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 
       45.67        18.21         8.52        74.53         6.08         9.24 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      122.30        37.91       115.69        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79         0.92        48.79        13.25        13.02        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       21.73         7.73        22.19         2.70        17.85         1.87 
TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N 
       23.41        64.57        14.33        39.45        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71        42.64         9.50         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-A94R 
        9.04         2.01        55.43         4.54        21.04        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       11.24        18.41        43.66        32.94        54.12        26.04 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 48(21Q11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-L5-A8NG 
       15.68        60.39        34.85        19.99        22.82        35.97 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GH 
        5.16        20.02        21.99        79.07        16.24        31.27 
TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE 
       14.30        58.55         8.94        16.24         4.21         7.69 
TCGA-IG-A3QL TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 
       35.21         2.63         9.30        17.03        23.41        12.82 
TCGA-IG-A7DP TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA TCGA-JY-A6FE TCGA-JY-A6FG 
       14.86         4.67        14.50        44.75         3.68        41.52 
TCGA-JY-A6FH TCGA-JY-A939 TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A4OO 
       47.38        21.70        25.22         6.28        21.01         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM 
        1.38         7.43        25.12        55.50        13.48         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U 
       21.37        83.24        10.45        12.66        12.33        15.35 
TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A8 
       12.59        12.46        12.59        12.49        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.33        25.25        10.52        12.33        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 
       12.03        12.26         7.59        16.31        53.95        15.78 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER 
        7.00         5.29         3.42        15.35        27.09        12.43 
TCGA-VR-A8EU TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I 
       18.31        33.70        18.18        18.05         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-3M-AB46 TCGA-B7-5816 
       18.21        25.08         3.42         1.32        58.03        26.70 
TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
       19.56         9.47         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6566 
       34.68        15.95        13.87        17.29        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        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 
       30.90        44.94        21.90         9.21        36.16        35.84 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.15        15.32         3.45         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       14.43         0.69        32.25         0.56        29.42         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-8370 TCGA-BR-8371 TCGA-BR-8372 
       22.19         0.95        26.33         3.32        11.80        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        7.36        25.05         3.72         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       32.58        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         8.98        14.17         0.53        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       32.52        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.18        13.35        11.21        12.59        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 
       12.59        11.64        15.39        12.07        12.43         6.31 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         7.99         8.05        14.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5720 TCGA-CG-5721 
        0.00         9.01         7.07        12.00         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5733 
        0.99       105.07        15.02        28.96        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        12.66        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 
       17.85        10.26        15.22        12.36        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19        18.21        14.66        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.44        20.32        22.29         8.38         4.34        19.96 
TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.13        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-7132 
       17.06        59.54         5.03        13.58         0.56        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       52.21        30.51         5.92        24.39        18.15        22.32 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        24.26        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.75        25.81        11.77        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        6.51         6.58        20.25         2.10        12.95        23.84 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       14.07        15.68         3.45        19.53         6.44        12.59 
TCGA-IN-A7NR TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A804 
        6.51        13.51         3.72        19.73        14.04         4.60 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         8.61         5.13        16.67        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E7 
       71.38        16.87        19.04         5.46        43.36        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT 
        2.50        12.79         9.27        15.65        13.35        29.59 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A927 
       73.41        11.70        21.83        32.88        60.85         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        5.72        66.81         2.66        28.41        38.93        17.13 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-ZA-A8F6 
       16.14        27.55        17.26 

  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                          0.23                           0.00 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                        122.30                         116.38 
  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE 
                        13.235                         14.760 
[1] "0.2 - 122.3 (13.2)" "0.0 - 116.4 (14.8)"
[1] "hr=" "1.1"
D86V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(21Q11.2) MUTATED         6        9       23       11        42
  DEL PEAK 48(21Q11.2) WILD-TYPE       4       12       24       22        45
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(21Q11.2) MUTATED          38        15         47         30
  DEL PEAK 48(21Q11.2) WILD-TYPE        49        13         48         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 48(21Q11.2) MUTATED           17       21         2
  DEL PEAK 48(21Q11.2) WILD-TYPE         29       28         2
D86V3, multiclass
            clus
vv           DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  STAGE I                               6                              4
  STAGE IA                              9                             12
  STAGE IB                             23                             24
  STAGE II                             11                             22
  STAGE IIA                            42                             45
  STAGE IIB                            38                             49
  STAGE III                            15                             13
  STAGE IIIA                           47                             48
  STAGE IIIB                           30                             42
  STAGE IIIC                           17                             29
  STAGE IV                             21                             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(21Q11.2) MUTATED      27  59 138  46
  DEL PEAK 48(21Q11.2) WILD-TYPE    28  77 145  78
D86V4, multiclass
       clus
vv      DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  T0+T1                           27                             28
  T2                              59                             77
  T3                             138                            145
  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 48(21Q11.2) MUTATED    94  90  47  36
  DEL PEAK 48(21Q11.2) WILD-TYPE 113  97  51  60
D86V5, multiclass
    clus
vv   DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  N0                           94                            113
  N1                           90                             97
  N2                           47                             51
  N3                           36                             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"
D86V6, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED   234  16
  DEL PEAK 48(21Q11.2) WILD-TYPE 290  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED    234   16
  DEL PEAK 48(21Q11.2) WILD-TYPE  290   23
   clus
vv  DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  0                          234                            290
  1                           16                             23
[1] 2 2
[1] FALSE
D86V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED    84 202
  DEL PEAK 48(21Q11.2) WILD-TYPE 101 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED     84  202
  DEL PEAK 48(21Q11.2) WILD-TYPE  101  238
        clus
vv       DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  FEMALE                           84                            101
  MALE                            202                            238
[1] 2 2
[1] FALSE
D86V8, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED   200  59
  DEL PEAK 48(21Q11.2) WILD-TYPE 245  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED    200   59
  DEL PEAK 48(21Q11.2) WILD-TYPE  245   60
     clus
vv    DEL PEAK 48(21Q11.2) MUTATED DEL PEAK 48(21Q11.2) WILD-TYPE
  NO                           200                            245
  YES                           59                             60
[1] 2 2
[1] FALSE
D86V9, continuous
D86V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(21Q11.2) MUTATED      55                         8
  DEL PEAK 48(21Q11.2) WILD-TYPE    79                         9
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(21Q11.2) MUTATED                                           0
  DEL PEAK 48(21Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 48(21Q11.2) MUTATED     183
  DEL PEAK 48(21Q11.2) WILD-TYPE   209
D86V11, multiclass
                                           clus
vv                                          DEL PEAK 48(21Q11.2) MUTATED
  ASIAN                                                               55
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              183
                                           clus
vv                                          DEL PEAK 48(21Q11.2) WILD-TYPE
  ASIAN                                                                 79
  BLACK OR AFRICAN AMERICAN                                              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, binary
                                cls
clus                               0   1
  DEL PEAK 48(21Q11.2) MUTATED     6 164
  DEL PEAK 48(21Q11.2) WILD-TYPE   5 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(21Q11.2) MUTATED      6  164
  DEL PEAK 48(21Q11.2) WILD-TYPE    5  240
                        clus
vv                       DEL PEAK 48(21Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          164
                        clus
vv                       DEL PEAK 48(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            240
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 49(21Q22.13) MUTATION ANALYSIS
D87V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 49(21Q22.13) MUTATED   176 120
  DEL PEAK 49(21Q22.13) WILD-TYPE 178 125
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                            296                             303 
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                            120                             125 
$`DEL PEAK 49(21Q22.13) MUTATED`
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y 
       18.28         4.31         8.94        24.00         4.70         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G 
       35.97        27.12        47.05        22.98         0.23        20.15 
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GK TCGA-2H-A9GM 
        9.86        27.35        26.93        25.78         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC 
        8.94        32.45        33.27         0.85        20.78        20.12 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A6QS TCGA-JY-A6F8 
       18.64         3.88         0.53         0.79         9.96       122.10 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A93C TCGA-JY-A93D TCGA-JY-A93E TCGA-JY-A93F 
       44.75        68.02        23.18        31.56        25.22        24.03 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4OM 
        3.16        30.25         0.30        32.61        21.01        47.93 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
        7.17         3.16        58.59         4.90        29.00         7.13 
TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 
        7.43        15.48         2.60         7.40         3.75         3.02 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NR 
        2.66        12.92        16.47        13.55        13.22         8.71 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49K 
       13.41        52.57        46.09        10.85        10.36         5.92 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A6 
       12.43        13.41        13.15        12.62        12.76        12.85 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        13.22        12.33        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        12.33        13.38        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A6XG 
        7.82         8.02         7.59         5.06         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-A7RC 
        6.35         9.30         2.89         2.30        12.69         3.42 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8ER 
       16.44         9.27         8.98        25.81        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4D 
        1.55         8.12        28.11        18.18        52.27        46.19 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
       11.24         9.17        25.08        41.23        14.37         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4184 
        2.66        19.73        11.70        11.01         9.44         6.97 
TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       18.35         4.08         9.67        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        33.63        39.78        28.73 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       33.21        14.43        11.44         9.60         8.05        19.96 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
       15.58         7.40        31.10        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        24.79        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
        9.86        20.88        10.68         7.53        34.98         1.48 
TCGA-BR-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        21.44        12.76        12.53         7.17        12.33 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       12.39        12.82        11.31        12.43        11.61        12.20 
TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 
       20.02        54.08         4.01        19.07        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
        7.07        30.97         6.97         1.02        12.03        15.02 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       65.10         4.01        69.04        20.91        19.13        20.55 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8578 
       13.35        17.19        15.98        12.79        11.31        21.14 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 
       14.27        16.44        11.31        15.65        19.96         0.62 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A9TM TCGA-HF-7133 
       72.23        11.38        19.53        17.06         6.21        63.06 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GC 
       26.47         1.51        28.96        22.82        22.68         3.25 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 
       11.77         8.98         6.58         0.26        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       23.84        23.80        21.17        36.36        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT 
       18.38        12.46        13.35         6.74         6.51        10.62 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       11.70        15.75         2.53         5.56        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
       36.95        14.04        45.67        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 
        6.08         9.24        16.67       122.30        37.91       115.69 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        19.04         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P5 
       48.79        13.25        13.02        18.48        37.41         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PX 
       46.26        22.19        17.85         1.87        23.41        64.57 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        39.45        61.22        18.74        20.81         1.71 
TCGA-VQ-A91V TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       42.64         9.73        55.56         2.01        55.43         4.54 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       66.81        21.04        42.54        11.24        18.41        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       38.93        32.94        17.13        54.12        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       12.43         0.79 

$`DEL PEAK 49(21Q22.13) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-Q9-A6FU 
       15.68        60.39        34.85        19.99        22.82         5.16 
TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-2H-A9GH TCGA-2H-A9GI 
       20.02        21.99        79.07        16.24        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RE TCGA-IG-A3QL 
       58.55         5.92        16.24         4.21         7.69        35.21 
TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A7DP 
        2.63         9.30        17.03        23.41        12.82        14.86 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
        4.67        14.50        12.16         3.68        41.52        47.38 
TCGA-JY-A939 TCGA-KH-A6WC TCGA-L5-A4OF TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
       21.70         6.28        26.33        18.35         3.32         1.38 
TCGA-L5-A88W TCGA-L5-A8NE TCGA-L5-A8NI TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
       25.12        55.50        13.48         7.76         5.49        21.37 
TCGA-L5-A8NU TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49U 
       83.24        10.45        12.66        12.33        13.38        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       12.59        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-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 
       13.18         0.13        12.03        16.31        53.95        15.78 
TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EU 
        7.00        20.38         5.29        15.35        27.09        18.31 
TCGA-VR-A8EY TCGA-VR-AA4G TCGA-VR-AA7I TCGA-X8-AAAR TCGA-Z6-A8JD TCGA-Z6-A9VB 
       33.70        18.05        15.91        18.21         3.42         1.32 
TCGA-3M-AB46 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 
       58.03        26.70        19.56         9.47         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 
        7.43        30.90         4.08         9.34         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 
        6.61        34.68        15.95        13.87        17.29        39.12 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        44.94        21.90         9.21        36.16 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       35.84        18.15        15.32         3.45         9.07        29.56 
TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
       37.25         0.69        29.59        32.25         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.66         2.20         6.18        13.08         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        0.95        26.33         3.32        11.80        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.05         3.72        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        9.34        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        8.22        34.13        13.87         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        8.98        14.17         0.53        28.34         0.66        32.52 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       16.14         5.13        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 
       13.35        11.21        12.10        12.59        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.43         6.31        12.30 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 
        1.02         7.99         8.05        14.01        29.98         0.00 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        9.01        12.00        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
      105.07        28.96        21.07         7.99        25.71        12.66 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 
       18.84        18.54        18.61        17.85        10.26        15.22 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       18.21        14.66        20.91         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        26.43        11.24        11.44        20.32        22.29 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
        8.38         4.34         7.13         7.99        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.48        14.07        22.29        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8243 
        0.56         5.52        77.29        52.21        30.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       24.39        18.15        22.32        21.07         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
        5.59        24.26        24.20        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H8 
       29.98         0.10         6.51        20.25         2.10        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       15.68        33.40         3.45        19.53         6.44        12.59 
TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BT 
       13.51         3.72        19.73         4.60        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DU 
        5.13        40.64       116.38        71.38        16.87         5.46 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       43.36        21.73        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.50        12.79         2.70         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91S 
       13.35        29.59        73.41        11.70        21.83        32.88 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P 
       60.85         9.50         9.04         6.58         5.72         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-ZA-A8F6 
       28.41        26.04        17.26 

  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                           0.23                            0.00 
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                         122.30                          116.38 
  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE 
                          13.46                           14.17 
[1] "0.2 - 122.3 (13.5)" "0.0 - 116.4 (14.2)"
[1] "hr=" "1.1"
D87V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(21Q22.13) MUTATED         7        9       24       11        41
  DEL PEAK 49(21Q22.13) WILD-TYPE       3       12       23       22        46
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(21Q22.13) MUTATED          41        16         51         32
  DEL PEAK 49(21Q22.13) WILD-TYPE        46        12         44         40
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 49(21Q22.13) MUTATED           21       22         2
  DEL PEAK 49(21Q22.13) WILD-TYPE         25       27         2
D87V3, multiclass
            clus
vv           DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  STAGE I                                7                               3
  STAGE IA                               9                              12
  STAGE IB                              24                              23
  STAGE II                              11                              22
  STAGE IIA                             41                              46
  STAGE IIB                             41                              46
  STAGE III                             16                              12
  STAGE IIIA                            51                              44
  STAGE IIIB                            32                              40
  STAGE IIIC                            21                              25
  STAGE IV                              22                              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
  DEL PEAK 49(21Q22.13) MUTATED      26  66 141  52
  DEL PEAK 49(21Q22.13) WILD-TYPE    29  70 142  72
D87V4, multiclass
       clus
vv      DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  T0+T1                            26                              29
  T2                               66                              70
  T3                              141                             142
  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 49(21Q22.13) MUTATED    96  94  46  46
  DEL PEAK 49(21Q22.13) WILD-TYPE 111  93  52  50
D87V5, multiclass
    clus
vv   DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  N0                            96                             111
  N1                            94                              93
  N2                            46                              52
  N3                            46                              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V6, binary
                                 cls
clus                                0   1
  DEL PEAK 49(21Q22.13) MUTATED   254  16
  DEL PEAK 49(21Q22.13) WILD-TYPE 270  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.13) MUTATED    254   16
  DEL PEAK 49(21Q22.13) WILD-TYPE  270   23
   clus
vv  DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  0                           254                             270
  1                            16                              23
[1] 2 2
[1] FALSE
D87V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(21Q22.13) MUTATED    88 217
  DEL PEAK 49(21Q22.13) WILD-TYPE  97 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.13) MUTATED     88  217
  DEL PEAK 49(21Q22.13) WILD-TYPE   97  223
        clus
vv       DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  FEMALE                            88                              97
  MALE                             217                             223
[1] 2 2
[1] FALSE
D87V8, binary
                                 cls
clus                                0   1
  DEL PEAK 49(21Q22.13) MUTATED   213  62
  DEL PEAK 49(21Q22.13) WILD-TYPE 232  57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.13) MUTATED    213   62
  DEL PEAK 49(21Q22.13) WILD-TYPE  232   57
     clus
vv    DEL PEAK 49(21Q22.13) MUTATED DEL PEAK 49(21Q22.13) WILD-TYPE
  NO                            213                             232
  YES                            62                              57
[1] 2 2
[1] FALSE
D87V9, continuous
D87V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(21Q22.13) MUTATED      58                        11
  DEL PEAK 49(21Q22.13) WILD-TYPE    76                         6
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 49(21Q22.13) MUTATED                                           0
  DEL PEAK 49(21Q22.13) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 49(21Q22.13) MUTATED     193
  DEL PEAK 49(21Q22.13) WILD-TYPE   199
D87V11, multiclass
                                           clus
vv                                          DEL PEAK 49(21Q22.13) MUTATED
  ASIAN                                                                58
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               193
                                           clus
vv                                          DEL PEAK 49(21Q22.13) WILD-TYPE
  ASIAN                                                                  76
  BLACK OR AFRICAN AMERICAN                                               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, binary
                                 cls
clus                                0   1
  DEL PEAK 49(21Q22.13) MUTATED     7 174
  DEL PEAK 49(21Q22.13) WILD-TYPE   4 230
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(21Q22.13) MUTATED      7  174
  DEL PEAK 49(21Q22.13) WILD-TYPE    4  230
                        clus
vv                       DEL PEAK 49(21Q22.13) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           174
                        clus
vv                       DEL PEAK 49(21Q22.13) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             230
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 50(22Q11.1) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 50(22Q11.1) MUTATED   126  96
  DEL PEAK 50(22Q11.1) WILD-TYPE 228 149
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                           222                            377 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                            96                            149 
$`DEL PEAK 50(22Q11.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88Y TCGA-CG-4444 
       34.85        18.28        24.00         4.70         0.36        47.05 
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U 
       21.99        16.24        20.15         9.86        27.35        26.93 
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-A93D TCGA-L5-A43C TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP 
       47.38        31.56         3.16        32.61        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88V 
        3.16        58.59         4.90        29.00         7.13         2.60 
TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.40         3.75         3.02        55.50         2.66        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NR 
       13.48        16.47        13.55        13.22         5.49         8.71 
TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O TCGA-LN-A49R 
       46.09        10.36         5.92        10.45        13.41        13.38 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A7HV TCGA-LN-A7HY 
       15.35        13.25        12.62        12.76        10.52        12.03 
TCGA-LN-A7HZ TCGA-LN-A8I1 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A8W5 
       13.18        13.18         8.02         7.59         5.06        15.78 
TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW 
        2.89         2.30         7.00         5.29        16.44         9.27 
TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-VR-A8EU TCGA-VR-A8EZ TCGA-XP-A8T8 TCGA-Z6-A8JE 
       25.81        22.82        18.31        18.18        14.37         2.10 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        2.66        19.73        58.03        11.01         9.44         6.61 
TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        4.08         9.67        17.29        19.33        26.10         9.17 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8058 
       12.16         9.21        33.63        39.78        28.73        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8484 
       14.43        11.44         9.60         7.40        14.04        25.18 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       26.73        24.79        32.58         8.22        10.68        13.87 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       34.98         0.72        32.52        20.65         1.15        21.44 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       13.15        13.35        12.76        12.53         7.17        12.39 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       15.39        12.07         6.31        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       12.20        20.02         3.02         8.05        54.08         4.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 
       29.98        19.07        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        20.91        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-FP-7829 
       16.44        11.31        15.65        19.96         0.62        19.53 
TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HU-8249 TCGA-HU-8604 
       17.06         0.56         5.52         6.21        28.96        22.82 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         6.58         0.26         2.10        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       23.80        21.17        33.40         3.39        18.38        12.46 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1V 
       19.53         6.44         6.74        12.59        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZR TCGA-R5-A805 
        2.53         5.56        14.04        45.67         6.08         9.24 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-SW-A7EB 
        8.61         5.13        16.67       115.69        35.61         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8PC 
       48.79         5.46        13.25        13.02        18.48        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91A 
       22.19        12.79        17.85         1.87        14.33        39.45 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y 
       18.74        20.81         1.71        42.64         9.50         9.73 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
        4.54        66.81        11.24        38.93        32.94         0.79 

$`DEL PEAK 50(22Q11.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 TCGA-CG-5727 
       35.97        27.12         5.16        20.02        22.98        79.07 
TCGA-FP-A8CX TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        0.23         7.69        33.27        35.21         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-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93C TCGA-JY-A93E TCGA-JY-A93F TCGA-KH-A6WC 
       41.52        21.70        23.18        25.22        24.03         6.28 
TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4OO 
       30.25         0.30        26.33        21.01        47.93         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A8NM TCGA-L5-A8NQ 
        1.38         7.43        15.48        25.12         7.76        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N 
       13.41        83.24        52.57        10.85        12.66        12.43 
TCGA-LN-A49P TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.33        13.15        12.59        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39        12.85        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX 
       13.22         4.47        12.33        25.25        12.00        12.23 
TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR 
       12.33        13.38         0.13        12.03        12.85        12.26 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ 
       33.11         7.82        16.31         7.04        38.40         6.35 
TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       53.95         9.30        12.69        20.38         3.42        15.35 
TCGA-V5-AASX TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EW TCGA-VR-A8EX 
        8.98        27.09        12.43         1.55         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        52.27        46.19        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JD TCGA-Z6-A9VB 
       15.91        18.21        25.08        41.23         3.42         1.32 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 
       26.70        11.70        19.56         9.47         6.97         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 
        7.43        18.35        30.90         4.08         9.34         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-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
       39.12        32.78        25.61        18.05        19.89         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       40.21        30.90        31.20        44.94        21.90        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       35.24        35.84        18.15        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       29.56        33.21         0.69        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.56        29.42         2.66        19.96         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        31.10        13.08         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        26.33         4.31         3.32        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 
       14.79         7.36        25.05         3.72         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        6.28         7.53        31.96         9.86        20.88        34.13 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        7.53         6.08         1.48        27.55        28.57        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98        14.17         0.53        28.34         0.66        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.42        16.14         5.13        13.41        13.02 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.18        11.21        12.10        12.59        12.33        12.30 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG 
       12.59        11.64        12.82        12.43        12.30         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       11.77        12.62        27.02        15.95         1.02         7.99 
TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       14.01        12.03         0.00         9.01         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
      105.07        28.96        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       25.71        19.13        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        12.36        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19        14.66        20.91        14.27         5.92        36.43 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        26.43        11.24        11.44        20.32 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       59.54         5.03        13.58        77.29        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       30.51        26.47         1.51         5.92        24.39        18.15 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       21.37        29.98         0.10         6.51        20.25        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RL 
       14.07        15.68        36.36         3.45        18.81        13.35 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J 
        6.51        10.62        13.51        63.62        37.64        36.95 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73        18.21         8.52        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05       122.30        37.91        40.64       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        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       34.29        16.31         2.50         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D 
       15.65        13.35        29.59        64.57        73.41        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
       21.83        61.22        32.88        60.85        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94P 
        2.01        55.43         6.58         5.72        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
       42.54        18.41        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                          0.26                           0.00 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                         122.1                          122.3 
  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE 
                        13.235                         14.760 
[1] "0.3 - 122.1 (13.2)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.2"
D88V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(22Q11.1) MUTATED         6        7       19       12        27
  DEL PEAK 50(22Q11.1) WILD-TYPE       4       14       28       21        60
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(22Q11.1) MUTATED          29        19         36         27
  DEL PEAK 50(22Q11.1) WILD-TYPE        58         9         59         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 50(22Q11.1) MUTATED           12       16         3
  DEL PEAK 50(22Q11.1) WILD-TYPE         34       33         1
D88V3, multiclass
            clus
vv           DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  STAGE I                               6                              4
  STAGE IA                              7                             14
  STAGE IB                             19                             28
  STAGE II                             12                             21
  STAGE IIA                            27                             60
  STAGE IIB                            29                             58
  STAGE III                            19                              9
  STAGE IIIA                           36                             59
  STAGE IIIB                           27                             45
  STAGE IIIC                           12                             34
  STAGE IV                             16                             33
  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 50(22Q11.1) MUTATED      28  43 119  30
  DEL PEAK 50(22Q11.1) WILD-TYPE    27  93 164  94
D88V4, multiclass
       clus
vv      DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  T0+T1                           28                             27
  T2                              43                             93
  T3                             119                            164
  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 50(22Q11.1) MUTATED    70  72  37  35
  DEL PEAK 50(22Q11.1) WILD-TYPE 137 115  61  61
D88V5, multiclass
    clus
vv   DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  N0                           70                            137
  N1                           72                            115
  N2                           37                             61
  N3                           35                             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"
D88V6, binary
                                cls
clus                               0   1
  DEL PEAK 50(22Q11.1) MUTATED   191  13
  DEL PEAK 50(22Q11.1) WILD-TYPE 333  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED    191   13
  DEL PEAK 50(22Q11.1) WILD-TYPE  333   26
   clus
vv  DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  0                          191                            333
  1                           13                             26
[1] 2 2
[1] FALSE
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 50(22Q11.1) MUTATED    62 168
  DEL PEAK 50(22Q11.1) WILD-TYPE 123 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED     62  168
  DEL PEAK 50(22Q11.1) WILD-TYPE  123  272
        clus
vv       DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  FEMALE                           62                            123
  MALE                            168                            272
[1] 2 2
[1] FALSE
D88V8, binary
                                cls
clus                               0   1
  DEL PEAK 50(22Q11.1) MUTATED   155  51
  DEL PEAK 50(22Q11.1) WILD-TYPE 290  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED    155   51
  DEL PEAK 50(22Q11.1) WILD-TYPE  290   68
     clus
vv    DEL PEAK 50(22Q11.1) MUTATED DEL PEAK 50(22Q11.1) WILD-TYPE
  NO                           155                            290
  YES                           51                             68
[1] 2 2
[1] FALSE
D88V9, continuous
D88V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 50(22Q11.1) MUTATED      43                         4
  DEL PEAK 50(22Q11.1) WILD-TYPE    91                        13
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 50(22Q11.1) MUTATED                                           1
  DEL PEAK 50(22Q11.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 50(22Q11.1) MUTATED     146
  DEL PEAK 50(22Q11.1) WILD-TYPE   246
D88V11, multiclass
                                           clus
vv                                          DEL PEAK 50(22Q11.1) MUTATED
  ASIAN                                                               43
  BLACK OR AFRICAN AMERICAN                                            4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              146
                                           clus
vv                                          DEL PEAK 50(22Q11.1) WILD-TYPE
  ASIAN                                                                 91
  BLACK OR AFRICAN AMERICAN                                             13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, binary
                                cls
clus                               0   1
  DEL PEAK 50(22Q11.1) MUTATED     4 136
  DEL PEAK 50(22Q11.1) WILD-TYPE   7 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 50(22Q11.1) MUTATED      4  136
  DEL PEAK 50(22Q11.1) WILD-TYPE    7  268
                        clus
vv                       DEL PEAK 50(22Q11.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 50(22Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            268
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 51(22Q13.31) MUTATION ANALYSIS
D89V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 51(22Q13.31) MUTATED   127 101
  DEL PEAK 51(22Q13.31) WILD-TYPE 227 144
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                            228                             371 
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                            101                             144 
$`DEL PEAK 51(22Q13.31) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-CG-4444 TCGA-CG-4460 
       34.85        18.28        24.00         4.70        47.05        21.99 
TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
       16.24        20.15         9.86        27.35        26.93        25.78 
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-IG-A3I8 TCGA-IG-A3YB 
        8.94        16.24         4.21        32.45        33.27         2.63 
TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A8O2 
       18.64         3.88         0.53         0.79        23.41         4.67 
TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OS 
      122.10        47.38        31.56        32.61         1.38        58.59 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NF 
        4.90        29.00         7.13         7.40         3.02         2.66 
TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NN 
       12.92        13.48        16.47        13.55        13.22         5.49 
TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49O 
        8.71        46.09        10.36         5.92        10.45        13.41 
TCGA-LN-A49R TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A9 
       13.38        15.35        13.25        12.62        12.76        11.54 
TCGA-LN-A7HV TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       10.52        12.03        13.18         8.02         7.59         5.06 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RB 
       38.40        53.95        15.78         2.89         7.00         5.29 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8EY 
       16.44         9.27        25.81        27.09        22.82        33.70 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN 
        2.10         2.66        19.73        58.03        11.01         9.44 
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-6456 
        6.61        18.35         4.08         9.67         6.18        17.29 
TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 
       19.33        26.10         9.17        12.16         9.21        33.63 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 
       37.25        14.43        11.44         0.69         9.60         2.20 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8677 
        7.40         6.18        31.10        14.04        25.18        26.73 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A4CQ 
       24.79        32.58         9.86         8.22        10.68        34.98 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       12.89         0.72        32.52        20.65         1.15        21.44 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 
       13.02        13.15        12.76        12.53        12.39        15.39 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       12.07         6.31        12.30        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-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 
       19.07        18.97        30.97        12.03        15.02        69.04 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       12.66        20.91        20.55        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 
       15.22        12.79        11.31        12.33        24.72        19.50 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A 
       18.21        21.14        16.44        11.31        15.65        19.96 
TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
        0.62        19.53        17.06         0.56         5.52         6.21 
TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY 
       63.06         5.92        28.96        22.75         8.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 
        2.10        12.95        23.84        21.17        33.40         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38        12.46        13.35        19.53         6.44         6.74 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-R5-A7O7 
       11.70        15.75         2.53         5.56        36.95        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
       18.21         6.08         8.61        16.67       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        48.79         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       18.48        43.36        37.22        46.26        22.19        12.79 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q 
       17.85         1.87        14.33        39.45        18.74        20.81 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 
        1.71        42.64         9.50         9.73         9.04         4.54 
TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       66.81        11.24        18.41        38.93        32.94         0.79 

$`DEL PEAK 51(22Q13.31) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         4.31         8.94        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 
        0.36        35.97        27.12         5.16        20.02        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-IC-A6RE TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
       79.07         0.23         7.69        35.21         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-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG 
       14.50        12.16        44.75        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-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON 
       30.25         0.30        26.33        21.01        47.93        18.35 
TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V 
        3.32         7.17         3.16         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NM TCGA-L5-A8NQ TCGA-L5-A8NS 
       25.12         3.75        55.50         7.76        21.37        13.41 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49P 
       83.24        52.57        10.85        12.66        12.43        12.33 
TCGA-LN-A49S TCGA-LN-A49V TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       13.15        12.59        12.46        12.59        12.49        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       22.39        12.85        15.52        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A8HZ TCGA-LN-A8I0 
       12.33        25.25        12.00        12.23        12.33        13.38 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18         0.13        12.03        12.85        12.26        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8WC 
        7.82        16.31         7.04         6.35         9.30         2.30 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-V5-AASX TCGA-VR-A8ER 
       12.69        20.38         3.42        15.35         8.98        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EZ TCGA-VR-A8Q7 
        1.55        18.31         8.12        28.11        18.18        52.27 
TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       46.19        18.05        11.24         9.17        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-B7-5816 
       25.08        41.23        14.37         3.42         1.32        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-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       30.90         4.08         9.34         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        40.21        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       44.94        21.90        36.16        35.24        35.84        39.78 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       18.15        15.32        28.73         3.45         9.07        29.56 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       33.21        29.59        32.25         8.05         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96        15.58        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T 
       28.14         6.28         7.53        31.96        20.88        34.13 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         7.53         6.08         1.48        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        8.98        14.17         0.53        28.34         0.66        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.46        20.42        16.14         5.13        13.41        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
       13.35        11.21        12.10        12.59         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG 
       12.30        12.59        11.64        12.82        12.43         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
        7.99        29.98        12.03         0.00         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       12.00         6.97        36.00         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 
        0.99       105.07        28.96        65.10         4.01        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        25.71        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 
       17.85        15.98        12.36        16.80        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        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A747 
       26.43        11.24        11.44        20.32        22.29         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        4.34         7.13         7.99        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-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-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58        77.29        52.21        30.51        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       24.39        18.15        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        6.58        20.25        29.00        23.80        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       36.36         3.45        18.81        12.59         6.51        10.62 
TCGA-IN-AB1X TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       13.51        63.62        37.64         3.72        19.73        14.04 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BW 
        8.52        74.53         4.60         9.24        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        37.91        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        8.94        16.87        19.04        21.73        37.41        38.14 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PJ 
        7.73        30.97        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        29.59        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91W 
       73.41        11.70        21.83        61.22        32.88        60.85 
TCGA-VQ-A91Z TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94O 
       55.56         2.01        55.43         6.58         5.72        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6D TCGA-VQ-AA6F 
        2.66        42.54        43.66        28.41        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                           0.26                            0.00 
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                          122.1                           122.3 
  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE 
                          13.25                           14.50 
[1] "0.3 - 122.1 (13.2)" "0.0 - 122.3 (14.5)"
[1] "hr=" "1.2"
D89V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(22Q13.31) MUTATED         6        2       19       12        29
  DEL PEAK 51(22Q13.31) WILD-TYPE       4       19       28       21        58
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(22Q13.31) MUTATED          28        18         42         30
  DEL PEAK 51(22Q13.31) WILD-TYPE        59        10         53         42
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 51(22Q13.31) MUTATED           14       17         3
  DEL PEAK 51(22Q13.31) WILD-TYPE         32       32         1
D89V3, multiclass
            clus
vv           DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  STAGE I                                6                               4
  STAGE IA                               2                              19
  STAGE IB                              19                              28
  STAGE II                              12                              21
  STAGE IIA                             29                              58
  STAGE IIB                             28                              59
  STAGE III                             18                              10
  STAGE IIIA                            42                              53
  STAGE IIIB                            30                              42
  STAGE IIIC                            14                              32
  STAGE IV                              17                              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 51(22Q13.31) MUTATED      19  47 119  39
  DEL PEAK 51(22Q13.31) WILD-TYPE    36  89 164  85
D89V4, multiclass
       clus
vv      DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  T0+T1                            19                              36
  T2                               47                              89
  T3                              119                             164
  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 51(22Q13.31) MUTATED    68  72  45  36
  DEL PEAK 51(22Q13.31) WILD-TYPE 139 115  53  60
D89V5, multiclass
    clus
vv   DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  N0                            68                             139
  N1                            72                             115
  N2                            45                              53
  N3                            36                              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"
D89V6, binary
                                 cls
clus                                0   1
  DEL PEAK 51(22Q13.31) MUTATED   203  12
  DEL PEAK 51(22Q13.31) WILD-TYPE 321  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 51(22Q13.31) MUTATED    203   12
  DEL PEAK 51(22Q13.31) WILD-TYPE  321   27
   clus
vv  DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  0                           203                             321
  1                            12                              27
[1] 2 2
[1] FALSE
D89V7, binary
                                 cls
clus                                0   1
  DEL PEAK 51(22Q13.31) MUTATED    64 171
  DEL PEAK 51(22Q13.31) WILD-TYPE 121 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 51(22Q13.31) MUTATED     64  171
  DEL PEAK 51(22Q13.31) WILD-TYPE  121  269
        clus
vv       DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  FEMALE                            64                             121
  MALE                             171                             269
[1] 2 2
[1] FALSE
D89V8, binary
                                 cls
clus                                0   1
  DEL PEAK 51(22Q13.31) MUTATED   166  50
  DEL PEAK 51(22Q13.31) WILD-TYPE 279  69
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 51(22Q13.31) MUTATED    166   50
  DEL PEAK 51(22Q13.31) WILD-TYPE  279   69
     clus
vv    DEL PEAK 51(22Q13.31) MUTATED DEL PEAK 51(22Q13.31) WILD-TYPE
  NO                            166                             279
  YES                            50                              69
[1] 2 2
[1] FALSE
D89V9, continuous
D89V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 51(22Q13.31) MUTATED      45                         3
  DEL PEAK 51(22Q13.31) WILD-TYPE    89                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 51(22Q13.31) MUTATED                                           1
  DEL PEAK 51(22Q13.31) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 51(22Q13.31) MUTATED     148
  DEL PEAK 51(22Q13.31) WILD-TYPE   244
D89V11, multiclass
                                           clus
vv                                          DEL PEAK 51(22Q13.31) MUTATED
  ASIAN                                                                45
  BLACK OR AFRICAN AMERICAN                                             3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               148
                                           clus
vv                                          DEL PEAK 51(22Q13.31) WILD-TYPE
  ASIAN                                                                  89
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, binary
                                 cls
clus                                0   1
  DEL PEAK 51(22Q13.31) MUTATED     3 142
  DEL PEAK 51(22Q13.31) WILD-TYPE   8 262
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 51(22Q13.31) MUTATED      3  142
  DEL PEAK 51(22Q13.31) WILD-TYPE    8  262
                        clus
vv                       DEL PEAK 51(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           142
                        clus
vv                       DEL PEAK 51(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             262
[1] 2 2
[1] FALSE

Clustering(90) Variable = DEL PEAK 52(XP22.2) MUTATION ANALYSIS
D90V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 52(XP22.2) MUTATED    94  54
  DEL PEAK 52(XP22.2) WILD-TYPE 260 191
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                          148                           451 
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                           54                           191 
$`DEL PEAK 52(XP22.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A4OE TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 
       34.85        18.28        24.00        20.02        47.05        21.99 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GI TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 
       27.35        26.93        14.30         4.21        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3YA TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5S3 
       35.21        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-A93C 
       12.82         9.96         4.67        44.75        47.38        23.18 
TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NJ 
       26.33        21.01        18.35         7.17         3.75        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-A49P TCGA-LN-A49R TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       12.33        13.38        12.62        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-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 
       13.18        13.38         0.13        12.85        12.26        33.11 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO 
       15.78         2.30        12.69         9.27         8.98        25.81 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR 
       18.31         8.12        18.18        52.27        15.91        18.21 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TN 
       25.08        14.37         3.42         2.10        58.03         9.44 
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8059 TCGA-BR-8289 TCGA-BR-8297 
       18.35        19.33        39.78        14.43         2.66         7.40 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8680 
       13.08        14.04         9.21        20.22         9.34        31.96 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4J6 TCGA-BR-A4PD 
        9.86        10.68        13.87        34.98         0.66        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8531 
        1.15        21.44        13.02        13.35        12.76        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 
       11.64        15.39        12.07        12.82        12.30        11.31 
TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5725 
       12.20        54.08        14.01        19.07        36.00        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        7.99        20.91        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.79        12.33        18.21        11.31        20.32        22.29 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4G3 
       15.65        19.96         0.62        13.58         5.52         5.59 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 
       22.75        25.81         6.58        23.80        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A93J TCGA-R5-A7O7 
        3.39        18.38        13.35         6.44        36.95        45.67 
TCGA-RD-A8N6 TCGA-VQ-A8P3 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.94        37.22        46.26        13.35         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6A 
        9.04         5.72        43.66        38.93 

$`DEL PEAK 52(XP22.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39         4.31         8.94         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-CG-4475 
       22.82         0.36        35.97        27.12         5.16        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GF 
       79.07        16.24         0.23        20.15         9.86        25.78 
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-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       16.24         7.69         0.85         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-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-A4OH 
       24.03         6.28         3.16        30.25         0.30        32.61 
TCGA-L5-A4OM TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
       47.93         3.32         1.38         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        12.92        13.48 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU 
       13.55        13.22         7.76         5.49        21.37        83.24 
TCGA-L5-A8NV TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       52.57        10.85        10.36        12.43        13.41        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       15.35        12.59        13.25        12.76        12.59        12.85 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY 
       15.52        11.54        12.33         4.47        12.23        12.03 
TCGA-LN-A8HZ TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ 
       12.33        13.18        12.03         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        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC 
        9.30         2.89         7.00        20.38         5.29         3.42 
TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8ET 
       16.44        15.35        27.09        22.82        12.43         1.55 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       28.11        33.70        46.19        18.05        11.24         9.17 
TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 
       41.23         1.32         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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
        7.43        30.90         4.08         4.08         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       17.29        13.68        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       25.61        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        44.94        21.90         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        33.63        18.15        15.32        28.73 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
        3.45         9.07        29.56        33.21        37.25        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       29.42        19.96         2.20        15.58         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19        17.52         0.95        26.33         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        3.32        11.80        31.27        14.79         7.36        25.05 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        25.18         1.12        12.79        27.12 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        24.79        32.58 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       20.88         8.22        34.13         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        28.34        32.52        13.51         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
       16.14         5.13        13.41        13.15        13.18        11.21 
TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
       12.10        12.59        12.53         7.17        12.33        12.30 
TCGA-CD-8530 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.39        12.43         6.31        12.43        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.77        12.62        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4455 
        1.02         7.99         8.05         4.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
        0.00         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       18.61        17.85        13.35        12.36        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19        14.66        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.24        11.44         8.38         4.34         7.13 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.99        14.47        72.23        21.27        11.38         3.48 
TCGA-FP-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-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
        0.56         6.21        77.29        63.06        52.21        30.51 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        24.39        18.15        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 
       22.32        22.82        21.07         0.76        24.30        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68        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        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       33.40        18.81        12.46        19.53         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.51        10.62        11.70        15.75        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        5.56        63.62        37.64         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PE 
       38.14         7.73        30.97        34.29        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        29.59        64.57        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       32.88         1.71        42.64        60.85         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P 
       55.43         4.54         6.58        66.81        21.04         2.66 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6D 
       42.54        11.24        18.41        28.41        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 
TCGA-ZQ-A9CR 
        0.79 

  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                        58.03                        122.30 
  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE 
                       13.725                        14.040 
[1] "0.1 - 58.0 (13.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D90V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP22.2) MUTATED         2        2        8       10        28
  DEL PEAK 52(XP22.2) WILD-TYPE       8       19       39       23        59
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP22.2) MUTATED          27         7         27         12
  DEL PEAK 52(XP22.2) WILD-TYPE        60        21         68         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 52(XP22.2) MUTATED            9        9         1
  DEL PEAK 52(XP22.2) WILD-TYPE         37       40         3
D90V3, multiclass
            clus
vv           DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             2                            19
  STAGE IB                             8                            39
  STAGE II                            10                            23
  STAGE IIA                           28                            59
  STAGE IIB                           27                            60
  STAGE III                            7                            21
  STAGE IIIA                          27                            68
  STAGE IIIB                          12                            60
  STAGE IIIC                           9                            37
  STAGE IV                             9                            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 52(XP22.2) MUTATED      11  39  72  24
  DEL PEAK 52(XP22.2) WILD-TYPE    44  97 211 100
D90V4, multiclass
       clus
vv      DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  T0+T1                          11                            44
  T2                             39                            97
  T3                             72                           211
  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 52(XP22.2) MUTATED    52  52  25  16
  DEL PEAK 52(XP22.2) WILD-TYPE 155 135  73  80
D90V5, multiclass
    clus
vv   DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  N0                          52                           155
  N1                          52                           135
  N2                          25                            73
  N3                          16                            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"
D90V6, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP22.2) MUTATED   129   8
  DEL PEAK 52(XP22.2) WILD-TYPE 395  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP22.2) MUTATED    129    8
  DEL PEAK 52(XP22.2) WILD-TYPE  395   31
   clus
vv  DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  0                         129                           395
  1                           8                            31
[1] 2 2
[1] FALSE
D90V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP22.2) MUTATED    30 121
  DEL PEAK 52(XP22.2) WILD-TYPE 155 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP22.2) MUTATED     30  121
  DEL PEAK 52(XP22.2) WILD-TYPE  155  319
        clus
vv       DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  FEMALE                          30                           155
  MALE                           121                           319
[1] 2 2
[1] FALSE
D90V8, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP22.2) MUTATED   107  31
  DEL PEAK 52(XP22.2) WILD-TYPE 338  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP22.2) MUTATED    107   31
  DEL PEAK 52(XP22.2) WILD-TYPE  338   88
     clus
vv    DEL PEAK 52(XP22.2) MUTATED DEL PEAK 52(XP22.2) WILD-TYPE
  NO                          107                           338
  YES                          31                            88
[1] 2 2
[1] FALSE
D90V9, continuous
D90V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 52(XP22.2) MUTATED      44                         2
  DEL PEAK 52(XP22.2) WILD-TYPE    90                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 52(XP22.2) MUTATED                                           0    91
  DEL PEAK 52(XP22.2) WILD-TYPE                                         1   301
D90V11, multiclass
                                           clus
vv                                          DEL PEAK 52(XP22.2) MUTATED
  ASIAN                                                              44
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              91
                                           clus
vv                                          DEL PEAK 52(XP22.2) WILD-TYPE
  ASIAN                                                                90
  BLACK OR AFRICAN AMERICAN                                            15
  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"
D90V12, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP22.2) MUTATED     5 101
  DEL PEAK 52(XP22.2) WILD-TYPE   6 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP22.2) MUTATED      5  101
  DEL PEAK 52(XP22.2) WILD-TYPE    6  303
                        clus
vv                       DEL PEAK 52(XP22.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         101
                        clus
vv                       DEL PEAK 52(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(91) Variable = DEL PEAK 53(XP21.1) MUTATION ANALYSIS
D91V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 53(XP21.1) MUTATED    83  61
  DEL PEAK 53(XP21.1) WILD-TYPE 271 184
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                          144                           455 
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                           61                           184 
$`DEL PEAK 53(XP21.1) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GI 
       47.05        21.99        27.35        26.93        25.78        14.30 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA 
        4.21        32.45        33.27        35.21         0.85        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-A93C TCGA-L5-A4OF TCGA-L5-A4OJ 
        4.67        44.75        47.38        23.18        26.33        21.01 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A891 TCGA-L5-A8NJ 
       47.93        18.35         7.17         1.38         3.75        16.47 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49Y 
       13.41         5.92        12.66        12.33        13.38        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4MR TCGA-LN-A5U6 TCGA-LN-A5U7 
       12.59        12.49        22.39        13.22        12.33        25.25 
TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A9FO TCGA-LN-A9FQ 
       10.52        12.00        13.18        13.38         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-R6-A8WG 
       12.26        33.11         8.02         2.89         2.30        12.69 
TCGA-V5-A7RB TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EU TCGA-VR-A8EW 
        5.29         9.27         8.98        25.81        18.31         8.12 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
       18.18        52.27        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
        3.42         2.10        58.03        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        19.96         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        34.98         0.66 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8532 TCGA-CD-8533 
       20.65         1.15        21.44        12.76        11.64        15.39 
TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 
       12.07        11.31        12.20         8.05        54.08        29.98 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 
       19.07         7.07        15.02         7.99        20.91        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        20.32        15.65        19.96         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        23.80         3.45         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-AB1X TCGA-KB-A93H TCGA-KB-A93J TCGA-R5-A7O7 
       13.35         6.44        13.51        37.64        36.95        45.67 
TCGA-RD-A8N6 TCGA-VQ-A8PC TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Z 
        8.94        46.26        13.35        14.33        18.74        55.56 
TCGA-VQ-A922 TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6J 
        9.04        18.41        43.66        38.93        17.13        27.55 

$`DEL PEAK 53(XP21.1) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        0.36        35.97        27.12        22.98        79.07        16.24 
TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK 
        0.23        20.15         9.86        31.27        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3YB 
        5.92        13.94         8.94        16.24         7.69         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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        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-A43H TCGA-L5-A4OH TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT 
        0.30        32.61         3.32         3.16        58.59         4.90 
TCGA-L5-A4OU TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
       29.00         7.13         7.43        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI 
        7.40         3.02        55.50         2.66        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-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L 
       83.24        52.57        46.09        10.85        10.36        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W 
       12.43        13.41        13.15        15.35        12.59        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.62        12.76        12.59        12.85        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A8HZ TCGA-LN-A8I1 
       12.33         4.47        12.23        12.03        12.33        13.18 
TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.03         7.82         7.59         5.06        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO 
       38.40         6.35        53.95         9.30        15.78         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ 
       20.38         3.42        16.44        15.35        27.09        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        33.70        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        41.23         1.32         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-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        4.31         3.32        11.80        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       25.05         3.72         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU 
        8.22        10.68        34.13         6.08         1.48        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       28.57        12.89         8.98         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
       28.34        32.52        13.51         0.46        20.42        16.14 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13        13.41        13.02        13.15        13.18        13.35 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       11.21        12.10        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
       12.30        12.39        12.59        12.82        12.43         6.31 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
       12.30        12.43        11.61         6.58        11.77        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
        4.01        14.01        12.03         0.00         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97        36.00         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
        4.01        69.04        21.07        25.71        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19        10.26 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6874 
       22.29         8.38         4.34         7.13         7.99        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27        11.38         3.48        19.53        14.07 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM 
       22.29        17.06        59.54         5.03         0.56         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       77.29        63.06        52.21        30.51        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        24.39        18.15        28.96        22.32        22.82 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       21.07         0.76        24.30         5.59        24.26        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.58        20.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.84        21.17        14.07 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN 
       15.68        33.40        36.36        18.81        12.46        19.53 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.74        12.59         6.51        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
        2.53         5.56        63.62         3.72        19.73        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       18.21         8.52        74.53         6.08         4.60         9.24 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         5.13        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.87        19.04         5.79         0.92        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       13.25        13.02        18.48        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       38.14        37.22         7.73        30.97        34.29        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       22.19         2.50        12.79         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        29.59        64.57        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91S 
       39.45        11.70        21.83        61.22        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A923 
        1.71        42.64        60.85         9.50         9.73         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O 
       55.43         4.54         6.58         5.72        66.81        21.04 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
        2.66        42.54        11.24        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       26.04        16.14        12.43        17.26         0.79 

  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                        58.03                        122.30 
  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE 
                       14.315                        13.780 
[1] "0.1 - 58.0 (14.3)"  "0.0 - 122.3 (13.8)"
[1] "hr=" "1.1"
D91V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XP21.1) MUTATED         2        3        6        7        26
  DEL PEAK 53(XP21.1) WILD-TYPE       8       18       41       26        61
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XP21.1) MUTATED          25         7         28         15
  DEL PEAK 53(XP21.1) WILD-TYPE        62        21         67         57
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 53(XP21.1) MUTATED            7        8         0
  DEL PEAK 53(XP21.1) WILD-TYPE         39       41         4
D91V3, multiclass
            clus
vv           DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             3                            18
  STAGE IB                             6                            41
  STAGE II                             7                            26
  STAGE IIA                           26                            61
  STAGE IIB                           25                            62
  STAGE III                            7                            21
  STAGE IIIA                          28                            67
  STAGE IIIB                          15                            57
  STAGE IIIC                           7                            39
  STAGE IV                             8                            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 53(XP21.1) MUTATED      13  35  67  24
  DEL PEAK 53(XP21.1) WILD-TYPE    42 101 216 100
D91V4, multiclass
       clus
vv      DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  T0+T1                          13                            42
  T2                             35                           101
  T3                             67                           216
  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 53(XP21.1) MUTATED    51  46  26  15
  DEL PEAK 53(XP21.1) WILD-TYPE 156 141  72  81
D91V5, multiclass
    clus
vv   DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  N0                          51                           156
  N1                          46                           141
  N2                          26                            72
  N3                          15                            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"
D91V6, binary
                               cls
clus                              0   1
  DEL PEAK 53(XP21.1) MUTATED   121   5
  DEL PEAK 53(XP21.1) WILD-TYPE 403  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XP21.1) MUTATED    121    5
  DEL PEAK 53(XP21.1) WILD-TYPE  403   34
   clus
vv  DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  0                         121                           403
  1                           5                            34
[1] 2 2
[1] FALSE
D91V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XP21.1) MUTATED    29 117
  DEL PEAK 53(XP21.1) WILD-TYPE 156 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XP21.1) MUTATED     29  117
  DEL PEAK 53(XP21.1) WILD-TYPE  156  323
        clus
vv       DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  FEMALE                          29                           156
  MALE                           117                           323
[1] 2 2
[1] FALSE
D91V8, binary
                               cls
clus                              0   1
  DEL PEAK 53(XP21.1) MUTATED   103  28
  DEL PEAK 53(XP21.1) WILD-TYPE 342  91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XP21.1) MUTATED    103   28
  DEL PEAK 53(XP21.1) WILD-TYPE  342   91
     clus
vv    DEL PEAK 53(XP21.1) MUTATED DEL PEAK 53(XP21.1) WILD-TYPE
  NO                          103                           342
  YES                          28                            91
[1] 2 2
[1] FALSE
D91V9, continuous
D91V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 53(XP21.1) MUTATED      35                         3
  DEL PEAK 53(XP21.1) WILD-TYPE    99                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 53(XP21.1) MUTATED                                           0    90
  DEL PEAK 53(XP21.1) WILD-TYPE                                         1   302
D91V11, multiclass
                                           clus
vv                                          DEL PEAK 53(XP21.1) MUTATED
  ASIAN                                                              35
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              90
                                           clus
vv                                          DEL PEAK 53(XP21.1) WILD-TYPE
  ASIAN                                                                99
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               302
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 53(XP21.1) MUTATED     6  89
  DEL PEAK 53(XP21.1) WILD-TYPE   5 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XP21.1) MUTATED      6   89
  DEL PEAK 53(XP21.1) WILD-TYPE    5  315
                        clus
vv                       DEL PEAK 53(XP21.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       DEL PEAK 53(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           315
[1] 2 2
[1] FALSE

Clustering(92) Variable = DEL PEAK 54(XP11.3) MUTATION ANALYSIS
D92V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 54(XP11.3) MUTATED    87  59
  DEL PEAK 54(XP11.3) WILD-TYPE 267 186
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                          146                           453 
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                           59                           186 
$`DEL PEAK 54(XP11.3) MUTATED`
TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-S8-A6BV 
       34.85        18.28         4.31        24.00         5.16        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF 
       47.05        21.99         0.23        27.35        26.93        25.78 
TCGA-2H-A9GI TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IG-A3QL TCGA-IG-A3Y9 
       14.30         8.94         4.21        32.45        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       20.78        20.12         3.88         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-JY-A6FA TCGA-JY-A6FH 
       23.41        12.82         9.96         4.67        44.75        47.38 
TCGA-JY-A93C TCGA-L5-A4OF TCGA-L5-A4OJ TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OP 
       23.18        26.33        21.01        47.93        18.35         7.17 
TCGA-L5-A891 TCGA-L5-A8NJ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49M 
        3.75        16.47         8.71        13.41         5.92        12.66 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       12.33        13.38        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A5 TCGA-LN-A4A9 TCGA-LN-A4MR TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.49        22.39        11.54        13.22        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.23        12.03        13.18        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-R6-A8W8 TCGA-R6-A8WC 
        0.13        12.85        12.26        33.11         2.89         2.30 
TCGA-R6-A8WG TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EU 
       12.69         9.27         8.98        25.81        27.09        18.31 
TCGA-VR-A8EW TCGA-VR-A8Q7 TCGA-VR-AA7I TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 
        8.12        52.27        15.91        18.21        25.08        14.37 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 
        3.42         2.10        58.03        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        19.96         7.40        13.08        17.52 
TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4QI TCGA-CD-8524 
        9.21         9.86        13.87        34.98        21.44        12.76 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       11.64        15.39        12.07        11.31        12.43        12.20 
TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5725 
        3.02         8.05        29.98        19.07         7.07        15.02 
TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        7.99        20.91        13.35        15.22        15.98        12.79 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 
       12.33        18.21        11.31        20.32        19.96         0.62 
TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4GD TCGA-HU-A4H2 TCGA-HU-A4H4 
        7.99        13.58         5.52        22.75        12.95        23.84 
TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL 
       23.80        36.36         3.45         3.39        18.38        13.35 
TCGA-IN-A6RP TCGA-KB-A93J TCGA-R5-A7O7 TCGA-RD-A8N6 TCGA-VQ-A8E0 TCGA-VQ-A8PC 
        6.44        36.95        45.67         8.94        18.48        46.26 
TCGA-VQ-A8PS TCGA-VQ-A8PY TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-AA68 
       13.35        14.33        18.74        55.56        66.81        43.66 
TCGA-VQ-AA6A TCGA-VQ-AA6D 
       38.93        17.13 

$`DEL PEAK 54(XP11.3) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       15.68        60.39         8.94         4.70        19.99        22.82 
TCGA-L5-A88Y TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO 
        0.36        35.97        27.12        22.98        79.07        16.24 
TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL 
       20.15         9.86        31.27        58.55         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GO TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3YB TCGA-IG-A4P3 
       13.94        16.24         7.69        33.27         2.63        18.64 
TCGA-IG-A4QT TCGA-IG-A7DP TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6F8 TCGA-JY-A6FD 
        9.30        14.86        14.50        12.16       122.10        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-A4OH TCGA-L5-A4OO 
        6.28         3.16        30.25         0.30        32.61         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-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 
        7.43        15.48         2.60        25.12         7.40         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NL 
       55.50         2.66        12.92        13.48        13.55        13.22 
TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
        7.76         5.49        21.37        83.24        52.57        46.09 
TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49S 
       10.85        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        12.59        12.76        12.59        12.85        15.52 
TCGA-LN-A4MQ TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A8HZ TCGA-LN-A9FP TCGA-Q9-A6FW 
       12.33         4.47        12.33        12.33        12.03         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        16.31         7.04        38.40 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-RE-A7BO TCGA-S8-A6BW 
        6.35        53.95         9.30        15.78         7.00        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASV TCGA-VR-A8EQ TCGA-VR-A8ER 
        5.29         3.42        16.44        15.35        22.82        12.43 
TCGA-VR-A8ET TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4D TCGA-VR-AA4G 
        1.55        28.11        33.70        18.18        46.19        18.05 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17        41.23         1.32         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-4253 TCGA-BR-4255 TCGA-BR-4256 
        4.64         7.43        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.87        17.29        13.68        39.12        26.10         9.17 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        25.61        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       40.21        30.90        31.20        44.94        21.90         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       36.16        35.24        35.84        33.63        39.78        18.15 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       15.32        28.73         3.45         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       37.25        11.44         0.69        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        8.05         0.56        29.42         2.66         2.20        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10         0.26        22.19         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32        11.80        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 
        7.36        25.05         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        27.12         9.34        28.14         6.28 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53        26.73        24.79        31.96        32.58        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
        8.22        10.68        34.13         7.53         6.08         1.48 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42         1.15        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.59        12.53         7.17        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
       12.59        12.82        12.43         6.31        12.30        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        6.58        11.77        12.62        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
        1.02         7.99        54.08         4.01        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        0.00         9.01        18.97        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        28.96        65.10         4.01        69.04        21.07 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       25.71        12.66        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 
       18.61        17.85        17.19        10.26        12.36        11.31 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        19.50        17.19        14.66        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.76        26.43        11.24        11.44        22.29        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-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-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-A4H3 
        6.51         6.58        20.25         0.26         2.10        29.00 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RJ 
       21.17        14.07        15.68        33.40        18.81        12.46 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       19.53         6.74        12.59         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       15.75        13.51         2.53         5.56        63.62        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        14.04        18.21         8.52        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        6.08         4.60         9.24        11.05         8.61         5.13 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-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        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-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        29.59 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         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        32.94        54.12        26.04        16.14        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                        66.81                        122.30 
  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE 
                       13.395                        14.040 
[1] "0.1 - 66.8 (13.4)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D92V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 54(XP11.3) MUTATED         2        3        7        7        28
  DEL PEAK 54(XP11.3) WILD-TYPE       8       18       40       26        59
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 54(XP11.3) MUTATED          25        11         27         13
  DEL PEAK 54(XP11.3) WILD-TYPE        62        17         68         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 54(XP11.3) MUTATED            8        7         0
  DEL PEAK 54(XP11.3) WILD-TYPE         38       42         4
D92V3, multiclass
            clus
vv           DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             3                            18
  STAGE IB                             7                            40
  STAGE II                             7                            26
  STAGE IIA                           28                            59
  STAGE IIB                           25                            62
  STAGE III                           11                            17
  STAGE IIIA                          27                            68
  STAGE IIIB                          13                            59
  STAGE IIIC                           8                            38
  STAGE IV                             7                            42
  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 54(XP11.3) MUTATED      12  36  73  21
  DEL PEAK 54(XP11.3) WILD-TYPE    43 100 210 103
D92V4, multiclass
       clus
vv      DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  T0+T1                          12                            43
  T2                             36                           100
  T3                             73                           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 54(XP11.3) MUTATED    53  49  24  15
  DEL PEAK 54(XP11.3) WILD-TYPE 154 138  74  81
D92V5, multiclass
    clus
vv   DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  N0                          53                           154
  N1                          49                           138
  N2                          24                            74
  N3                          15                            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"
D92V6, binary
                               cls
clus                              0   1
  DEL PEAK 54(XP11.3) MUTATED   123   6
  DEL PEAK 54(XP11.3) WILD-TYPE 401  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 54(XP11.3) MUTATED    123    6
  DEL PEAK 54(XP11.3) WILD-TYPE  401   33
   clus
vv  DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  0                         123                           401
  1                           6                            33
[1] 2 2
[1] FALSE
D92V7, binary
                               cls
clus                              0   1
  DEL PEAK 54(XP11.3) MUTATED    30 118
  DEL PEAK 54(XP11.3) WILD-TYPE 155 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 54(XP11.3) MUTATED     30  118
  DEL PEAK 54(XP11.3) WILD-TYPE  155  322
        clus
vv       DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  FEMALE                          30                           155
  MALE                           118                           322
[1] 2 2
[1] FALSE
D92V8, binary
                               cls
clus                              0   1
  DEL PEAK 54(XP11.3) MUTATED   100  33
  DEL PEAK 54(XP11.3) WILD-TYPE 345  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 54(XP11.3) MUTATED    100   33
  DEL PEAK 54(XP11.3) WILD-TYPE  345   86
     clus
vv    DEL PEAK 54(XP11.3) MUTATED DEL PEAK 54(XP11.3) WILD-TYPE
  NO                          100                           345
  YES                          33                            86
[1] 2 2
[1] FALSE
D92V9, continuous
D92V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 54(XP11.3) MUTATED      41                         3
  DEL PEAK 54(XP11.3) WILD-TYPE    93                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 54(XP11.3) MUTATED                                           0    86
  DEL PEAK 54(XP11.3) WILD-TYPE                                         1   306
D92V11, multiclass
                                           clus
vv                                          DEL PEAK 54(XP11.3) MUTATED
  ASIAN                                                              41
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              86
                                           clus
vv                                          DEL PEAK 54(XP11.3) WILD-TYPE
  ASIAN                                                                93
  BLACK OR AFRICAN AMERICAN                                            14
  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"
D92V12, binary
                               cls
clus                              0   1
  DEL PEAK 54(XP11.3) MUTATED     5  92
  DEL PEAK 54(XP11.3) WILD-TYPE   6 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 54(XP11.3) MUTATED      5   92
  DEL PEAK 54(XP11.3) WILD-TYPE    6  312
                        clus
vv                       DEL PEAK 54(XP11.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 54(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(93) Variable = DEL PEAK 55(XQ11.2) MUTATION ANALYSIS
D93V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 55(XQ11.2) MUTATED    61  42
  DEL PEAK 55(XQ11.2) WILD-TYPE 293 203
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                          103                           496 
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                           42                           203 
$`DEL PEAK 55(XQ11.2) MUTATED`
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-CG-4444 
       34.85         8.94        24.00         0.36         5.16        47.05 
TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-IG-A3YC 
        0.23        27.35        26.93        25.78         4.21        20.12 
TCGA-IG-A6QS TCGA-JY-A6FA TCGA-JY-A6FH TCGA-JY-A93C TCGA-L5-A4OF TCGA-L5-A4OJ 
        9.96        44.75        47.38        23.18        26.33        21.01 
TCGA-L5-A4OP TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NR 
        7.17         3.75        13.48        16.47        13.55         8.71 
TCGA-L5-A8NS TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49Y TCGA-LN-A4A2 
       13.41         5.92        10.45        12.66        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FQ 
       22.39        25.25        10.52        13.38        13.18        12.85 
TCGA-M9-A5M8 TCGA-R6-A8WC TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASW TCGA-V5-AASX 
       33.11         2.30         5.29         3.42         9.27         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-AA7B TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-3M-AB46 
       25.81        12.43        11.24        18.21        25.08        58.03 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-8058 
       11.70        19.56         9.44        18.35        19.33        37.25 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8365 TCGA-BR-8678 TCGA-BR-8680 
       19.96        31.10        13.08        17.52        24.79        31.96 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4PF TCGA-CD-8527 
       13.87         7.53        34.98         1.48         1.15         7.17 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 
       11.64        15.39        12.07        11.31        20.02         3.02 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6518 
       29.98        19.07         7.07        36.00        15.02        19.13 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A6EZ TCGA-D7-A74A 
       15.22        15.98        12.79        18.21        20.32        19.96 
TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 
        7.99        13.58         5.52        23.80        36.36         3.39 
TCGA-IN-A6RI TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A93J TCGA-RD-A8MV TCGA-RD-A8N6 
       18.38         6.44         6.74        36.95       122.30         8.94 
TCGA-VQ-A8E0 TCGA-VQ-A8PS TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-AA68 TCGA-VQ-AA6A 
       18.48        13.35        18.74        20.81        43.66        38.93 
TCGA-VQ-AA6D 
       17.13 

$`DEL PEAK 55(XQ11.2) WILD-TYPE`
TCGA-IC-A6RF TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A4OG TCGA-L5-A4OI 
       15.68        60.39        18.28         4.31         4.70        19.99 
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 
       22.82        35.97        27.12        20.02        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH TCGA-2H-A9GI 
       79.07        16.24        20.15         9.86        31.27        14.30 
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO 
       58.55         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-A3YA 
       32.45         7.69        33.27        35.21         0.85        20.78 
TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A51D 
        2.63        18.64         3.88         9.30         0.53        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-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A939 
       12.16       122.10        68.02         3.68        41.52        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-A43H TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ 
        0.30        32.61        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-A4OX 
        3.16        58.59         4.90        29.00         7.13         7.43 
TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE 
       15.48         2.60        25.12         7.40         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NL TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NQ 
        2.66        12.92        13.22         7.76         5.49        21.37 
TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A56G TCGA-L7-A6VZ TCGA-LN-A49N 
       83.24        52.57        46.09        10.85        10.36        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V 
       13.41        12.33        13.38        13.15        15.35        12.59 
TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 
       13.25        12.62        12.59        12.76        12.59        12.85 
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-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A9FO 
       12.00        12.23        12.03        13.18        12.33         0.13 
TCGA-LN-A9FP TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ 
       12.03        12.26         7.82         8.02         7.59         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 
       16.31         7.04        38.40         6.35        53.95         9.30 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BW TCGA-V5-A7RE 
       15.78         2.89        12.69         7.00        20.38        16.44 
TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW 
       15.35        27.09        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        33.70        18.18        52.27        46.19        18.05 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
        9.17        15.91        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-A5TJ TCGA-B7-A5TK 
        1.32         2.66        19.73        26.70        11.01         9.47 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64         7.43        30.90         4.08 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
        4.08         9.34         9.67         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
       34.68        15.95        13.87        17.29        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       26.10         9.17        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
       12.16         8.98        40.21        30.90        31.20        44.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       21.90         9.21        36.16        35.24        35.84        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 
       39.78        18.15        15.32        28.73         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       29.56        33.21        14.43        11.44         0.69        29.59 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        9.60        32.25         8.05         0.56        29.42         2.66 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-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 
       31.27        14.79         7.36        25.05         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
       25.18         9.21        20.22         1.12        12.79        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 
        9.34        28.14         6.28         7.53        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
        9.86        20.88         8.22        10.68        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       27.55        28.57        12.89         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        21.44        16.14         5.13        13.41 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.02        13.15        13.18        13.35        11.21        12.10 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53        12.33        12.30        12.39 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       12.59        12.82        12.43         6.31        12.30        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        11.77        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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       14.01        12.03         0.00         9.01        18.97        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        12.03        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       10.26        12.36        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-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        36.43        13.78        14.76        26.43 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       11.24        11.31        11.44        22.29        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-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       11.38         3.48        19.53        14.07        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03         0.56         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       18.15        28.96        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-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         6.58        20.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        21.17        14.07        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       33.40         3.45        18.81        12.46        13.35        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        63.62        37.64         3.72        19.73 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.04        45.67        18.21         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        4.60         9.24        11.05         8.61         5.13        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       35.61        16.87        19.04         5.79         0.92        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       16.31        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        29.59        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        73.41        39.45        11.70        21.83        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       32.88         1.71        42.64        60.85         9.50         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
       55.56         9.04         2.01        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T 
        5.72        66.81        21.04         2.66        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       18.41        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                         0.23                          0.00 
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                        122.3                         122.1 
  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE 
                       15.220                        13.825 
[1] "0.2 - 122.3 (15.2)" "0.0 - 122.1 (13.8)"
[1] "hr=" "1"  
D93V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 55(XQ11.2) MUTATED         2        3        6        7        16
  DEL PEAK 55(XQ11.2) WILD-TYPE       8       18       41       26        71
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 55(XQ11.2) MUTATED          16         6         16          8
  DEL PEAK 55(XQ11.2) WILD-TYPE        71        22         79         64
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 55(XQ11.2) MUTATED            8        6         0
  DEL PEAK 55(XQ11.2) WILD-TYPE         38       43         4
D93V3, multiclass
            clus
vv           DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  STAGE I                              2                             8
  STAGE IA                             3                            18
  STAGE IB                             6                            41
  STAGE II                             7                            26
  STAGE IIA                           16                            71
  STAGE IIB                           16                            71
  STAGE III                            6                            22
  STAGE IIIA                          16                            79
  STAGE IIIB                           8                            64
  STAGE IIIC                           8                            38
  STAGE IV                             6                            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 55(XQ11.2) MUTATED      10  28  43  19
  DEL PEAK 55(XQ11.2) WILD-TYPE    45 108 240 105
D93V4, multiclass
       clus
vv      DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  T0+T1                          10                            45
  T2                             28                           108
  T3                             43                           240
  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 55(XQ11.2) MUTATED    34  32  19  14
  DEL PEAK 55(XQ11.2) WILD-TYPE 173 155  79  82
D93V5, multiclass
    clus
vv   DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  N0                          34                           173
  N1                          32                           155
  N2                          19                            79
  N3                          14                            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"
D93V6, binary
                               cls
clus                              0   1
  DEL PEAK 55(XQ11.2) MUTATED    87   3
  DEL PEAK 55(XQ11.2) WILD-TYPE 437  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 55(XQ11.2) MUTATED     87    3
  DEL PEAK 55(XQ11.2) WILD-TYPE  437   36
   clus
vv  DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  0                          87                           437
  1                           3                            36
[1] 2 2
[1] FALSE
D93V7, binary
                               cls
clus                              0   1
  DEL PEAK 55(XQ11.2) MUTATED    24  81
  DEL PEAK 55(XQ11.2) WILD-TYPE 161 359
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 55(XQ11.2) MUTATED     24   81
  DEL PEAK 55(XQ11.2) WILD-TYPE  161  359
        clus
vv       DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  FEMALE                          24                           161
  MALE                            81                           359
[1] 2 2
[1] FALSE
D93V8, binary
                               cls
clus                              0   1
  DEL PEAK 55(XQ11.2) MUTATED    67  26
  DEL PEAK 55(XQ11.2) WILD-TYPE 378  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 55(XQ11.2) MUTATED     67   26
  DEL PEAK 55(XQ11.2) WILD-TYPE  378   93
     clus
vv    DEL PEAK 55(XQ11.2) MUTATED DEL PEAK 55(XQ11.2) WILD-TYPE
  NO                           67                           378
  YES                          26                            93
[1] 2 2
[1] FALSE
D93V9, continuous
D93V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 55(XQ11.2) MUTATED      22                         3
  DEL PEAK 55(XQ11.2) WILD-TYPE   112                        14
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 55(XQ11.2) MUTATED                                           0    62
  DEL PEAK 55(XQ11.2) WILD-TYPE                                         1   330
D93V11, multiclass
                                           clus
vv                                          DEL PEAK 55(XQ11.2) MUTATED
  ASIAN                                                              22
  BLACK OR AFRICAN AMERICAN                                           3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              62
                                           clus
vv                                          DEL PEAK 55(XQ11.2) WILD-TYPE
  ASIAN                                                               112
  BLACK OR AFRICAN AMERICAN                                            14
  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"
D93V12, binary
                               cls
clus                              0   1
  DEL PEAK 55(XQ11.2) MUTATED     3  62
  DEL PEAK 55(XQ11.2) WILD-TYPE   8 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 55(XQ11.2) MUTATED      3   62
  DEL PEAK 55(XQ11.2) WILD-TYPE    8  342
                        clus
vv                       DEL PEAK 55(XQ11.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 55(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           342
[1] 2 2
[1] FALSE

Clustering(94) Variable = DEL PEAK 56(XQ21.33) MUTATION ANALYSIS
D94V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 56(XQ21.33) MUTATED    62  35
  DEL PEAK 56(XQ21.33) WILD-TYPE 292 210
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                            97                            502 
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                            35                            210 
$`DEL PEAK 56(XQ21.33) MUTATED`
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A88Y TCGA-CG-4444 
       15.68        34.85        18.28         8.94         0.36        47.05 
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GQ TCGA-JY-A6FH TCGA-L5-A4OJ 
       27.35        26.93        25.78         4.21        47.38        21.01 
TCGA-L5-A4OM TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NJ 
       47.93         7.17         3.16         3.75        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-LN-A49M TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A2 
       13.55        13.22        12.66        13.25        12.46        12.49 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A9 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HY 
       22.39        12.85        11.54        25.25        10.52        12.03 
TCGA-LN-A9FO TCGA-M9-A5M8 TCGA-R6-A6KZ TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO 
        0.13        33.11         5.06         2.89         2.30         7.00 
TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EO TCGA-VR-AA7B 
        3.42        16.44         9.27         8.98        25.81        11.24 
TCGA-XP-A8T6 TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN 
       25.08        19.73        58.03        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        39.78        37.25        19.96        31.10        17.52 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       24.79        31.96        13.87         7.53        34.98         1.48 
TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8534 
       13.51        13.15         7.17        12.30        11.64        12.07 
TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 
       11.31        20.02         3.02         7.99        29.98        19.07 
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8575 
        7.07        15.02        20.55        15.22        12.33        18.21 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-8211 TCGA-HF-7133 
       11.31        20.32        19.96         7.99        13.58        63.06 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-VQ-A8DT 
       23.80        33.40        36.36        18.38         6.74        48.79 
TCGA-VQ-A8E0 TCGA-VQ-A8P5 TCGA-VQ-A8PS TCGA-VQ-A91Q TCGA-VQ-A91X TCGA-VQ-AA6A 
       18.48         7.73        13.35        20.81         9.50        38.93 
TCGA-VQ-AA6D 
       17.13 

$`DEL PEAK 56(XQ21.33) WILD-TYPE`
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88T 
       60.39         4.31        24.00         4.70        19.99        22.82 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4460 TCGA-CG-4475 
       35.97        27.12         5.16        20.02        21.99        22.98 
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GH 
       79.07        16.24         0.23        20.15         9.86        31.27 
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-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       16.24        32.45         7.69        33.27        35.21         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-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-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-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-A4OF TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS 
       26.33        32.61        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-A88V 
        4.90        29.00         7.13         7.43        15.48         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
       25.12         7.40         3.02        55.50         2.66        12.92 
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-A56G TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L 
       52.57        46.09        10.85        10.36         5.92        10.45 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49X TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A8 
       12.59        12.62        12.59        12.76        12.59        15.52 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A7HW TCGA-LN-A7HX 
       12.33        13.22         4.47        12.33        12.00        12.23 
TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FP TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18        12.03        12.85 
TCGA-LN-A9FR TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26         7.82         8.02         7.59        16.31         7.04 
TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
       38.40         6.35        53.95         9.30        15.78        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER 
       20.38         5.29        15.35        27.09        22.82        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        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4D TCGA-VR-AA4G TCGA-VR-AA7D TCGA-VR-AA7I TCGA-X8-AAAR 
       52.27        46.19        18.05         9.17        15.91        18.21 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         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-4253 TCGA-BR-4255 TCGA-BR-4256 
        7.43        18.35        30.90         4.08         4.08         9.34 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
        9.67         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        9.17        32.78        25.61        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        40.21        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       36.16        35.24        35.84        33.63        18.15        15.32 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       28.73         3.45         9.07        29.56        33.21        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       11.44         0.69        29.59         9.60        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.56        29.42         2.66         2.20        15.58         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
        6.18        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        31.27        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        7.36        25.05         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        27.12         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        6.28         7.53        26.73        32.58         9.86        20.88 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        8.22        10.68        34.13         6.08        27.55        28.57 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         8.98         0.72        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        32.52         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 
       21.44        16.14         5.13        13.41        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
       12.33        12.39        12.59        15.39        12.82        12.43 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.31        12.30        12.43        11.61         6.58        12.20 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       11.77        12.62        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       54.08         4.01        14.01        12.03         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97        12.00        30.97         6.97        36.00         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 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 
       12.36        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
       14.66        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       36.43        13.78        14.76        26.43        11.24        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         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-8631 
       14.07        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        5.52         6.21        77.29        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        24.39        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.82        21.07         0.76        24.30         5.59        24.26 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       22.68        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       20.25         0.26         2.10        12.95        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       21.17        14.07        15.68         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35        19.53         6.44        12.59         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
       10.62        11.70        15.75        13.51         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       63.62        37.64        36.95         3.72        19.73        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
       45.67        18.21         8.52        74.53         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        9.24        11.05         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
        8.94        35.61        16.87        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        5.46        13.25        13.02        43.36        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       38.14        37.22        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-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        29.59        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       73.41        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       32.88         1.71        42.64        60.85         9.73        55.56 
TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.04         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 
       66.81        21.04         2.66        42.54        11.24        18.41 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                         63.06                         122.30 
  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE 
                        13.580                         14.025 
[1] "0.1 - 63.1 (13.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D94V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 56(XQ21.33) MUTATED         2        5        9        7        14
  DEL PEAK 56(XQ21.33) WILD-TYPE       8       16       38       26        73
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 56(XQ21.33) MUTATED          11         7         14          6
  DEL PEAK 56(XQ21.33) WILD-TYPE        76        21         81         66
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 56(XQ21.33) MUTATED            5        7         0
  DEL PEAK 56(XQ21.33) WILD-TYPE         41       42         4
D94V3, multiclass
            clus
vv           DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  STAGE I                               2                              8
  STAGE IA                              5                             16
  STAGE IB                              9                             38
  STAGE II                              7                             26
  STAGE IIA                            14                             73
  STAGE IIB                            11                             76
  STAGE III                             7                             21
  STAGE IIIA                           14                             81
  STAGE IIIB                            6                             66
  STAGE IIIC                            5                             41
  STAGE IV                              7                             42
  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 56(XQ21.33) MUTATED      10  23  45  14
  DEL PEAK 56(XQ21.33) WILD-TYPE    45 113 238 110
D94V4, multiclass
       clus
vv      DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  T0+T1                           10                             45
  T2                              23                            113
  T3                              45                            238
  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 56(XQ21.33) MUTATED    39  27  13  11
  DEL PEAK 56(XQ21.33) WILD-TYPE 168 160  85  85
D94V5, multiclass
    clus
vv   DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  N0                           39                            168
  N1                           27                            160
  N2                           13                             85
  N3                           11                             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"
D94V6, binary
                                cls
clus                               0   1
  DEL PEAK 56(XQ21.33) MUTATED    78   4
  DEL PEAK 56(XQ21.33) WILD-TYPE 446  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 56(XQ21.33) MUTATED     78    4
  DEL PEAK 56(XQ21.33) WILD-TYPE  446   35
   clus
vv  DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  0                           78                            446
  1                            4                             35
[1] 2 2
[1] FALSE
D94V7, binary
                                cls
clus                               0   1
  DEL PEAK 56(XQ21.33) MUTATED    24  74
  DEL PEAK 56(XQ21.33) WILD-TYPE 161 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 56(XQ21.33) MUTATED     24   74
  DEL PEAK 56(XQ21.33) WILD-TYPE  161  366
        clus
vv       DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  FEMALE                           24                            161
  MALE                             74                            366
[1] 2 2
[1] FALSE
D94V8, binary
                                cls
clus                               0   1
  DEL PEAK 56(XQ21.33) MUTATED    62  24
  DEL PEAK 56(XQ21.33) WILD-TYPE 383  95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 56(XQ21.33) MUTATED     62   24
  DEL PEAK 56(XQ21.33) WILD-TYPE  383   95
     clus
vv    DEL PEAK 56(XQ21.33) MUTATED DEL PEAK 56(XQ21.33) WILD-TYPE
  NO                            62                            383
  YES                           24                             95
[1] 2 2
[1] FALSE
D94V9, continuous
D94V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN
  DEL PEAK 56(XQ21.33) MUTATED      21                         3
  DEL PEAK 56(XQ21.33) WILD-TYPE   113                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 56(XQ21.33) MUTATED                                           0
  DEL PEAK 56(XQ21.33) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 56(XQ21.33) MUTATED      58
  DEL PEAK 56(XQ21.33) WILD-TYPE   334
D94V11, multiclass
                                           clus
vv                                          DEL PEAK 56(XQ21.33) MUTATED
  ASIAN                                                               21
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               58
                                           clus
vv                                          DEL PEAK 56(XQ21.33) WILD-TYPE
  ASIAN                                                                113
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                334
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 56(XQ21.33) MUTATED     2  57
  DEL PEAK 56(XQ21.33) WILD-TYPE   9 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 56(XQ21.33) MUTATED      2   57
  DEL PEAK 56(XQ21.33) WILD-TYPE    9  347
                        clus
vv                       DEL PEAK 56(XQ21.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 56(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE
